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| Contents | Index |
| Learn more about Bioinformatics Toolbox |
This table summarizes what's new in Version 3.0 (R2007b):
| New Features and Changes | Version Compatibility Considerations | Fixed Bugs and Known Problems | Related Documentation at Web Site |
|---|---|---|---|
| Yes Details below | Yes—Details labeled as Compatibility Considerations, below. See also Summary. | Bug
Reports Includes fixes | No |
New and updated features in this version include:
Following are new functions:
blastformat — Create local BLAST database.
blastreadlocal — Read data from local BLAST report.
cytobandread — Read cytogenetic banding information.
The following function was updated:
affyread — Read microarray data from Affymetrix GeneChip file. Updated the structure returned when reading a CDF library file. The structure contains three new subfields: GroupNumber, Direction, and GroupName.
Following is a new function:
cytobandread — Read cytogenetic banding information.
The following function was updated:
affyread — Read microarray data from Affymetrix GeneChip file. Updated the structure returned when reading a CDF library file. The structure contains three new subfields: GroupNumber, Direction, and GroupName.
Following are new functions:
chromosomeplot — Plot chromosome ideogram with G-banding pattern.
cghcbs — Perform circular binary segmentation (CBS) on array-based comparative genomic hybridization (aCGH) data.
The following function is updated:
probesetvalues — Create table of Affymetrix probe set intensity values. Updated return matrix, which contains intensity values for probe-level data, to include two new fields: GroupNumber and Direction. Updated to return a second output containing the column names for the return matrix, which contains intensity values for probe-level data.
Following are new functions:
blastlocal — Perform search on local BLAST database to create BLAST report.
rnaconvert — Convert secondary structure of RNA sequence between bracket and matrix notations.
rnafold — Predict minimum free-energy secondary structure of RNA sequence.
rnaplot — Draw secondary structure of RNA sequence.
The following function is updated:
mspalign — Align mass spectra from multiple peak lists from LC/MS or GC/MS data set. Updated to include a new property, 'ShowEstimation', which controls the display of an assessment plot relative to the estimation method and the vector of common mass/charge (m/z) values.
The following function is updated:
svmsmoset — Create or edit Sequential Minimal Optimization (SMO) options structure. Updated default values for the 'MaxIter' and 'KernelCacheLimit' properties. Changed the 'Display' property so that when set to 'iter', a report displays every 500 iterations instead of 10.
In Bioinformatics Toolbox Version 2.6 and earlier, the svmsmoset function used a 'MaxIter' property with a default of 1500 and a 'KernelCacheLimit' property with a default of 7500. In Bioinformatics Toolbox Version 3.0, the defaults are 15000 and 5000, respectively. Also, when you set the 'Display' property to 'iter', a report displays every 500 iterations instead of 10.
The following methods of a gene ontology object are updated:
geneont.getancestors — Find terms that are ancestors of specified Gene Ontology term. Updated to also return the number of times each ancestor is found. Updated to include two new properties, 'Relationtype', which specifies a relationship type to search for in the gene ontology, and 'Exclude', which controls excluding the original queried term(s) from the output, unless the term was reached while searching the gene ontology.
geneont.getdescendants — Find terms that are descendants of specified Gene Ontology term. Updated to also return the number of times each descendant is found. Updated to include two new properties, 'Relationtype', which specifies a relationship type to search for in the gene ontology, and 'Exclude', which controls excluding the original queried term(s) from the output, unless the term was reached while searching the gene ontology.
geneont.getrelatives — Find terms that are relatives of specified Gene Ontology term. Updated to also return the number of times each relative is found. Updated to include three new properties, 'Levels', which specifies the number of levels up and down to search in the gene ontology, 'Relationtype', which specifies a relationship type to search for in the gene ontology, and 'Exclude', which controls excluding the original queried term(s) from the output, unless the term was reached while searching the gene ontology.
The following are two new microarray data analysis demos:
Detecting DNA Copy Number Alteration in Array-Based CGH Data
Analyzing Array-Based CGH Data Using Bayesian Hidden Markov Modeling
The following are two new sequence analysis demos:
The Investigating the Bird Flu Virus demo was updated to demonstrate how to write KML-formatted files, which can be used by Google™ Earth to display geospatial data.
The following is a new graph theory demo:
 | Version 3.1 (R2008a) Bioinformatics Toolbox Software | Version 2.6 (R2007a+) Bioinformatics Toolbox Software |  |
Includes the most popular MATLAB recorded presentations with Q&A sessions led by MATLAB experts.
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