Version 2.3 (R2006a+) Bioinformatics Toolbox™ Software Release Notes

Version 2.3 (R2006a+) Bioinformatics Toolbox™ Software

This table summarizes what's new in Version 2.3 (Release 2006a+):

New functions, obsoleted functions, and changes introduced in this version are

• Data Formats and Databases Functions

• Sequence Utilities Functions

• Sequence Visualization Functions

• Statistical Learning Functions

• Microarray Functions

• Demo for Microarray Functions

Data Formats and Databases Functions

The following functions are obsolete:

• getpir — Sequence data from PIR-PSD database. This function retrieved data from the PIR-PSD database. This database has been discontinued and this function no longer retrieves data. See http://pir.georgetown.edu/pirwww/dbinfo/nref.shtml for more details.

• pirread — Read data from Protein Information Resource (PIR) file. This function supported the data format of the PIR-PSD database. This database has been discontinued. See http://pir.georgetown.edu/pirwww/dbinfo/nref.shtml for more details.

Sequence Utilities Functions

The following function was updated to include five new databases, including refseq_rna, refseq_genomic, env_nt, refseq_protein, and env_nr:

• blastncbi — Generate remote BLAST request.

Sequence Visualization Functions

Following is a new function for visualizing sequence data:

• featuresmap — Draw linear or circular map of features from GenBank^® structure.

Statistical Learning Functions

The following function was updated to include three new properties, including RBF_Sigma, BoxConstraint, and Autoscale:

• svmtrain — Train support vector machine classifier.

Microarray Functions

The following function is supported on the Windows^® 32 platform only:

• affyread — Read microarray data from Affymetrix^® GeneChip^® file (Windows 32).

Following are new functions for preprocessing Affymetrix probe-level microarray data:

• celintensityread — Read probe intensities from Affymetrix CEL files (Windows 32).

• rmabackadj — Perform background adjustment on Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure.

• rmasummary — Calculate gene (probe set) expression values from Affymetrix microarray probe-level data using Robust Multi-array Average (RMA) procedure.

• affyinvarsetnorm — Perform rank invariant set normalization on probe intensities from multiple Affymetrix CEL or DAT files.

Following is a new function for two-color microarray normalization:

• mainvarsetnorm — Perform rank invariant set normalization on gene expression values from two experimental conditions or phenotypes.

Following are new functions for microarray differential expression analysis:

• mattest — Perform two-sample, two-tailed t-test to evaluate differential expression of genes from two experimental conditions or phenotypes.

• mavolcanoplot — Create significance versus gene expression ratio (fold change) scatter plot of microarray data.

Demo for Microarray Functions

New demo of the new microarray functions (Analyzing Affymetrix Microarray Gene Expression Data).

Version 2.4 (R2006b) Bioinformatics Toolbox™ Software

Version 2.2.1 (R2006a) Bioinformatics Toolbox™ Software