{"group":{"id":1,"name":"Community","lockable":false,"created_at":"2012-01-18T18:02:15.000Z","updated_at":"2026-04-06T14:01:22.000Z","description":"Problems submitted by members of the MATLAB Central community.","is_default":true,"created_by":161519,"badge_id":null,"featured":false,"trending":false,"solution_count_in_trending_period":0,"trending_last_calculated":"2026-04-06T00:00:00.000Z","image_id":null,"published":true,"community_created":false,"status_id":2,"is_default_group_for_player":false,"deleted_by":null,"deleted_at":null,"restored_by":null,"restored_at":null,"description_opc":null,"description_html":null,"published_at":null},"problems":[{"id":797,"title":"Genome Sequence 003R: Sequence DNA of random positioned and flipped segments","description":"This is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments. DNA Sequencing is naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssGCCATGGACATCsssss Middle Rev\r\nssssCTACAGGTACCGsssss Middle flipped\r\nssssssssssssGACATTACG\r\nGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\r\nSegments may be reversed (Change from 003)\r\nSegments start at random positions\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 726.633px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.317px; transform-origin: 407px 363.317px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 341px 8px; transform-origin: 341px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 133.5px 8px; transform-origin: 133.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 368.5px 8px; transform-origin: 368.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 128px 8.5px; transform-origin: 128px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssGCCATGGACATCsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 40px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 40px 8.5px; \"\u003eMiddle Rev\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 144px 8.5px; transform-origin: 144px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 56px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 56px 8.5px; \"\u003eMiddle flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 382px 8px; transform-origin: 382px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 163.467px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 81.7333px; transform-origin: 391px 81.7333px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 148.5px 8px; transform-origin: 148.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be reversed (Change from 003)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 111.5px 8px; transform-origin: 111.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 324.5px 8px; transform-origin: 324.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 84px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 42px; text-align: left; transform-origin: 384px 42px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 355.5px 8px; transform-origin: 355.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003R(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=563*17;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2021-07-16T14:52:10.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-06-27T17:37:02.000Z","updated_at":"2021-07-16T14:52:10.000Z","published_at":"2012-10-07T22:51:12.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssGCCATGGACATCsssss Middle Rev\\nssssCTACAGGTACCGsssss Middle flipped\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be reversed (Change from 003)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":969,"title":"Genome Sequence 003: DNA Sequence with random positioned segments","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssCTACAGGTACCGsssss Middle\r\nssssssssssssGACATTACG\r\nGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\r\nSegments start at random positions (Genome_003 change from 001)\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 706.767px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 353.383px; transform-origin: 407px 353.383px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 366.5px 8px; transform-origin: 366.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 81.7333px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 40.8667px; transform-origin: 404px 40.8667px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 217px 8px; transform-origin: 217px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions (Genome_003 change from 001)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 250px 8px; transform-origin: 250px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 345.5px 8px; transform-origin: 345.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=1024;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":"2021-07-16T14:46:09.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-10-03T04:17:33.000Z","updated_at":"2025-05-05T20:24:45.000Z","published_at":"2012-10-03T04:47:11.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssCTACAGGTACCGsssss Middle\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions (Genome_003 change from 001)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"}],"problem_search":{"errors":[],"problems":[{"id":797,"title":"Genome Sequence 003R: Sequence DNA of random positioned and flipped segments","description":"This is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments. DNA Sequencing is naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssGCCATGGACATCsssss Middle Rev\r\nssssCTACAGGTACCGsssss Middle flipped\r\nssssssssssssGACATTACG\r\nGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\r\nSegments may be reversed (Change from 003)\r\nSegments start at random positions\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 726.633px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.317px; transform-origin: 407px 363.317px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 341px 8px; transform-origin: 341px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 133.5px 8px; transform-origin: 133.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 368.5px 8px; transform-origin: 368.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 128px 8.5px; transform-origin: 128px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssGCCATGGACATCsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 40px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 40px 8.5px; \"\u003eMiddle Rev\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 144px 8.5px; transform-origin: 144px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 56px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 56px 8.5px; \"\u003eMiddle flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 382px 8px; transform-origin: 382px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 163.467px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 81.7333px; transform-origin: 391px 81.7333px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 148.5px 8px; transform-origin: 148.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be reversed (Change from 003)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 111.5px 8px; transform-origin: 111.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 324.5px 8px; transform-origin: 324.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 84px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 42px; text-align: left; transform-origin: 384px 42px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 355.5px 8px; transform-origin: 355.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003R(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=563*17;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2021-07-16T14:52:10.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-06-27T17:37:02.000Z","updated_at":"2021-07-16T14:52:10.000Z","published_at":"2012-10-07T22:51:12.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssGCCATGGACATCsssss Middle Rev\\nssssCTACAGGTACCGsssss Middle flipped\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be reversed (Change from 003)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":969,"title":"Genome Sequence 003: DNA Sequence with random positioned segments","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssCTACAGGTACCGsssss Middle\r\nssssssssssssGACATTACG\r\nGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\r\nSegments start at random positions (Genome_003 change from 001)\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 706.767px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 353.383px; transform-origin: 407px 353.383px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 366.5px 8px; transform-origin: 366.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 81.7333px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 40.8667px; transform-origin: 404px 40.8667px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 217px 8px; transform-origin: 217px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions (Genome_003 change from 001)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 250px 8px; transform-origin: 250px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 345.5px 8px; transform-origin: 345.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=1024;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":"2021-07-16T14:46:09.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-10-03T04:17:33.000Z","updated_at":"2025-05-05T20:24:45.000Z","published_at":"2012-10-03T04:47:11.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssCTACAGGTACCGsssss Middle\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions (Genome_003 change from 001)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc 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