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| R2011b Documentation → Bioinformatics Toolbox | |
Learn more about Bioinformatics Toolbox |
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| Contents | Index |
This table summarizes what's new in Version 3.6 (R2010b):
| New Features and Changes | Version Compatibility Considerations | Fixed Bugs and Known Problems |
|---|---|---|
| Yes Details below | Yes—Details labeled as Compatibility Considerations, below. See also Summary. | Bug
Reports Includes fixes |
New and updated features in this version include:
The following new functions allow indexed file access to BAM-formatted files:
bamindexread — Read Binary Sequence Alignment/Map Index (BAI) file.
baminfo — Return information about Binary Sequence Alignment/Map (BAM) file.
bamread — Read data from Binary Sequence Alignment/Map (BAM) file.
The following new functions let you read Bowtie- and SOAP-formatted files:
bowtieread — Read data from Bowtie file.
soapread — Read data from Short Oligonucleotide Analysis Package (SOAP) file.
The following new functions support CIGAR strings for sequence mapping and alignment:
align2cigar — Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings.
cigar2align — Convert unaligned sequences to aligned sequences using Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings
The following functions are updated:
aacount — Count amino acids in sequence. Updated by adding the Ambiguous property, which lets you specify how to count ambiguous amino acid characters. Updated by adding the Gaps property, which lets you specify to count or ignore gaps. The Others and Structure properties still work, but display a warning, indicating that they will be invalid in future versions of Bioinformatics Toolbox. The Others field in the output structure is replaced by the Ambiguous field.
basecount — Count nucleotides in sequence. Updated by adding the Ambiguous property, which lets you specify how to count ambiguous nucleotide characters. Updated by adding the Gaps property, which lets you specify to count or ignore gaps. The Others and Structure properties still work, but display a warning, indicating that they will be invalid in future versions of Bioinformatics Toolbox. The Others field in the output structure is replaced by the Ambiguous field.
codonbias — Calculate codon frequency for each amino acid coded for in nucleotide sequence. Updated by adding the Ambiguous property, which lets you specify how to count codons containing ambiguous nucleotide characters.
codoncount — Count codons in nucleotide sequence. Updated by adding the Ambiguous property, which lets you specify how to count codons containing ambiguous nucleotide characters. Updated by adding the GeneticCode property, which lets you overlay a grid that groups the synonymous codons on the heat map of the codon counts. The Others field in the output structure is replaced by the Ambiguous field.
dimercount — Count dimers in nucleotide sequence. Updated by adding the Ambiguous property, which lets you specify how to count dimers containing ambiguous nucleotide characters. The Others field in the output structure is replaced by the Ambiguous field.
In Bioinformatics Toolbox Version 3.5 and earlier, the aacount and basecount functions included 'Others' and 'Structure' property name/property value pairs, which let you specify how to count ambiguous characters and gaps, and whether to display a warning. These functions also returned a structure with an Others field.
In Bioinformatics Toolbox Version 3.6, the aacount and basecount functions still allow 'Others' and 'Structure' property name/property value pairs, but display a warning. Now the aacount and basecount functions include the 'Ambiguous' and 'Gaps' property name/property value pairs, which specify whether to count or ignore ambiguous characters and gaps, as well as specify how to count ambiguous characters, and whether to display a warning. These functions now return a structure with an Ambiguous field, which replaces the Others field.
In Bioinformatics Toolbox Version 3.6, the codoncount and dimercount functions return a structure with an optional Ambiguous field, which replaces the Others field.
The following function is updated:
nwalign — Globally align two sequences using Needleman-Wunsch algorithm. Updated to support semiglobal or "glocal" alignments by addition of Glocal property.
The following new functions support CIGAR strings for sequence mapping and alignment:
align2cigar — Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings.
cigar2align — Convert unaligned sequences to aligned sequences using Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings
The following functions are updated:
multialign — Align multiple sequences using progressive method. Updated to include a new property, 'UseParallel', which lets you use parfor-loops and compute in parallel mode.
seqpdist — Calculate pairwise distance between sequences. Updated to include a new property, 'UseParallel', which lets you use parfor-loops and compute in parallel mode.
In Bioinformatics Toolbox Version 3.4 and earlier, the multialign and seqpdist functions included 'JobManager' and 'WaitInQueue' property name/property value pairs, which let you process in parallel, including support for the MATLAB scheduler for clusters.
In Bioinformatics Toolbox Version 3.5, the multialign and seqpdist functions allowed the 'JobManager' and 'WaitInQueue' property name/property value pairs, but displayed a warning.
In Bioinformatics Toolbox Version 3.6, the multialign and seqpdist functions error if you use the 'JobManager' or 'WaitInQueue' property name/property value pair. Instead they include the 'UseParallel' property name/property value pair, which lets you process in parallel, including support for:
Local workers for multicore machines
The MATLAB scheduler for clusters
Third-party schedulers for clusters
You can now create a BioMap object from a MATLAB structure containing sequence and alignment information, returned by the bamread function.
The following method of the BioMap class is updated:
| getCoverage — Compute read coverage in BioMap object. Updated to return the coverage of multiple regions of the reference sequence. |
The BioMap class includes the following new methods:
getCompactAlignment — Construct compact alignment represented in BioMap object.
getMatePosition — Retrieve mate positions of read sequences from BioMap object.
setMatePosition — Set mate positions of read sequences in BioMap object.
The BioMap class includes the following new property:
MatePosition — Positions of the mates for all read sequences represented in the BioMap object.
| Function Element Name | What Happens When You Use This Function Element | Use This Instead | Compatibility Considerations |
|---|---|---|---|
| 'Others' property name/property value pair as input to aacount and basecount functions | Warns | 'Ambiguous' or 'Gaps' property name/property value pair as input to aacount and basecount functions | See the Compatibility Considerations subheading in Sequence Statistics Functions. |
| 'Structure' property name/property value pair as input to aacount and basecount functions | Warns | 'Ambiguous' property name/property value pair with either 'ignore' or 'warn' as input to aacount and basecount functions | See the Compatibility Considerations subheading in Sequence Statistics Functions. |
| 'JobManager' property name/property value pair as input to multialign and seqpdist functions | Errors | 'UseParallel' property name/property value pair as input to multialign and seqpdist functions | See the Compatibility Considerations subheading in Multiple Sequence Alignment Functions. |
| 'WaitInQueue' property name/property value pair as input to multialign and seqpdist functions | Errors | 'UseParallel' property name/property value pair as input to multialign and seqpdist functions | See the Compatibility Considerations subheading in Multiple Sequence Alignment Functions. |
The following properties of a clustergram object:
| Errors | New properties of a clustergram object:
| See Clustergram Methods and Properties. |
| 'Dimension' property name/property value pair as input to clustergram function | Errors | 'Cluster' property name/property value pair as input to clustergram function | See the Compatibility Considerations subheading in Microarray Functions. |
| 'Pdist' property name/property value pair as input to clustergram function | Errors | Either 'RowPdist' or 'ColumnPdist' property name/property value pair as input to clustergram function | See the Compatibility Considerations subheading in Microarray Functions. |
| pdbplot function | Errors | molviewer function | See the Compatibility Considerations subheading in Protein Analysis and Sequence Utilities Functions. |
| getpir and pirread functions | Errors | Use getembl, getgenpept, and getpdb to retrieve protein sequences from Web databases. Use emblread, genpeptread, and pdbread to read protein sequence data. | See Data Formats and Databases Functions. |
| mamadnorm and mameannorm functions | Errors | manorm function | See Microarray Analysis. |
 | Version 3.7 (R2011a) Bioinformatics Toolbox Software | Version 3.5 (R2010a) Bioinformatics Toolbox Software |  |
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