| Bioinformatics Toolbox™ | |
seqshoworfs(SeqNT)
seqshoworfs(SeqNT,
...'Frames', FramesValue, ...)
seqshoworfs(SeqNT, ...'GeneticCode', GeneticCodeValue, ...)
seqshoworfs(SeqNT, ...'MinimumLength', MinimumLengthValue, ...)
seqshoworfs(SeqNT, ...'AlternativeStartCodons', AlternativeStartCodonsValue, ...)
seqshoworfs(SeqNT, ...'Color', ColorValue, ...)
seqshoworfs(SeqNT, ...'Columns', ColumnsValue, ...)
| SeqNT | Nucleotide sequence. Enter either a character string with the characters A, T (U), G, C, and ambiguous characters R, Y, K, M, S, W, B, D, H, V, N, or a vector of integers. You can also enter a structure with the field Sequence. |
| FramesValue | Property to select the frame. Enter 1, 2, 3, -1, -2, -3, enter a vector with integers, or 'all'. The default value is the vector [1 2 3]. Frames -1, -2, and -3 correspond to the first, second, and third reading frames for the reverse complement. |
| GeneticCodeValue | Genetic code name. Enter a code number or a code name from the table Genetic Code. |
| MinimumLengthValue | Property to set the minimum number of codons in an ORF. |
| AlternativeStartCodonsValue | Property to control using alternative start codons. Enter either true or false. The default value is false. |
| ColorValue | Property to select the color for highlighting the reading frame. Enter either a 1-by-3 RGB vector specifying the intensity (0 to 255) of the red, green, and blue components of the color, or a character from the following list: 'b'—blue, 'g'—green, 'r'—red, 'c'—cyan, 'm'—magenta, or 'y'—yellow. To specify different colors for the three reading frames, use a 1-by-3 cell array of color values. If you are displaying reverse complement reading frames, then COLOR should be a 1-by-6 cell array of color values. |
| ColumnsValue | Property to specify the number of columns in the output. |
Genetic Code
| Code Number | Code Name |
|---|---|
| 1 | Standard |
| 2 | Vertebrate Mitochondrial |
| 3 | Yeast Mitochondrial |
| 4 | Mold, Protozoan, Coelenterate Mitochondrial, and Mycoplasma/Spiroplasma |
| 5 | Invertebrate Mitochondrial |
| 6 | Ciliate, Dasycladacean, and Hexamita Nuclear |
| 9 | Echinoderm Mitochondrial |
| 10 | Euplotid Nuclear |
| 11 | Bacterial and Plant Plastid |
| 12 | Alternative Yeast Nuclear |
| 13 | Ascidian Mitochondrial |
| 14 | Flatworm Mitochondrial |
| 15 | Blepharisma Nuclear |
| 16 | Chlorophycean Mitochondrial |
| 21 | Trematode Mitochondrial |
| 22 | Scenedesmus Obliquus Mitochondrial |
| 23 | Thraustochytrium Mitochondrial |
seqshoworfs identifies and highlights all open reading frames using the standard or an alternative genetic code.
seqshoworfs(SeqNT) displays the sequence with all open reading frames highlighted, and it returns a structure of start and stop positions for each ORF in each reading frame. The standard genetic code is used with start codon 'AUG' and stop codons 'UAA', 'UAG', and 'UGA'.
seqshoworfs(SeqNT, ...'PropertyName', PropertyValue, ...) calls seqshoworfs with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotes and is case insensitive. These property name/property value pairs are as follows:
seqshoworfs(SeqNT,
...'Frames', FramesValue, ...) specifies
the reading frames to display. The default is to display the first,
second, and third reading frames with ORFs highlighted in each frame.
seqshoworfs(SeqNT, ...'GeneticCode', GeneticCodeValue, ...) specifies the genetic code to use for finding open reading frames.
seqshoworfs(SeqNT, ...'MinimumLength', MinimumLengthValue, ...) sets the minimum number of codons for an ORF to be considered valid. The default value is 10.
seqshoworfs(SeqNT, ...'AlternativeStartCodons', AlternativeStartCodonsValue, ...) uses alternative start codons if AlternativeStartCodons is set to true. For example, in the human mitochondrial genetic code, AUA and AUU are known to be alternative start codons. For more details on alternative start codons, see
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
seqshoworfs(SeqNT, ...'Color', ColorValue, ...) specifies the color used to highlight the open reading frames in the output display. The default color scheme is blue for the first reading frame, red for the second, and green for the third frame.
seqshoworfs(SeqNT, ...'Columns', ColumnsValue, ...) specifies how many columns per line to use in the output. The default value is 64.
Look for the open reading frames in a random nucleotide sequence.
s = randseq(200, 'alphabet', 'dna'); seqshoworfs(s);
Identify the open reading frames in a GenBank sequence.
HLA_DQB1 = getgenbank('NM_002123');
seqshoworfs(HLA_DQB1.Sequence);
Bioinformatics Toolbox functions: codoncount, cpgisland, geneticcode, seqdisp, seqshowwords, seqtool, seqwordcount
MATLAB function: regexp
| seqreverse | seqshowwords | |
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