Version 3.2 (R2008b) Bioinformatics Toolbox Software :: Bioinformatics Toolbox Release Notes (Bioinformatics Toolbox)

Version 3.2 (R2008b) Bioinformatics Toolbox Software

This table summarizes what's new in Version 3.2 (R2008b):

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:

Data Format and Database Functions

Following are new functions:

affygcrma — Perform GC Robust Multi-array Average (GCRMA) procedure on Affymetrix microarray probe-level data.
affyrma — Perform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data.
affysnpannotread — Read Affymetrix Mapping DNA array data from CSV-formatted annotation file.
geoseriesread — Read Gene Expression Omnibus (GEO) Series (GSE) format data.
multialignwrite — Write multiple-alignment to file using ClustalW ALN format.
mzcdfread — Read mass spectrometry data from netCDF file.

The following functions are updated:

affyread — Read microarray data from Affymetrix GeneChip file. Updated so that Probes field in the return structure is now a single, which reduces memory usage.
celintensityread — Read probe intensities from Affymetrix CEL files. Updated so that PMIntensities and MMIntensities fields in the return structure are now singles, which reduces memory usage.
geosoftread — Read Gene Expression Omnibus (GEO) SOFT format data. Updated to support Platform (GPL) records.
getgeodata — Retrieve Gene Expression Omnibus (GEO) format data. Updated to support Platform (GPL) and Series (GSE) records.
goannotread — Read annotations from Gene Ontology annotated file. Updated to include two new properties, 'Fields' and 'Aspect', which let you read a subset of the data in the annotated file.
multialignread — Read multiple sequence alignment file. Updated to support PHYLIP (Phylogeny Inference Package) multiple-sequence alignment files.
mzxmlread — Read data from mzXML file. Improved to read larger files, faster and without running out of memory. Updated with three new properties, 'Levels', 'TimeRange', and 'ScanIndices', which let you filter and read a subset of the data. Updated with a 'Verbose' property to control the progress display while reading the file.

Compatibility Considerations

In Bioinformatics Toolbox Version 3.1 and earlier, the Probes field, in the structure returned by affyread, and the PMIntensities and MMIntensities fields, in the structure returned by celintensityread, were doubles. In Bioinformatics Toolbox Version 3.2, these fields are singles.

Sequence Utility Functions

Following is a new function:

cleavelookup — Find cleavage rule for enzyme or compound.

The following functions are updated:

blastncbi — Create remote NCBI BLAST report request ID or link to NCBI BLAST report. Updated to include a 'GapCosts' property, which lets you specify penalties for both opening and extending gaps, and an 'Entrez' property, which lets you limit searches using Entrez query syntax.
cleave — Cleave amino acid sequence with enzyme. Includes a new input argument that specifies the name of an enzyme or compound for which a cleavage rule is specified in the literature.
rebasecuts — Find restriction enzymes that cut nucleotide sequence. Updated to use Version 806 of REBASE, the Restriction Enzyme Database.
restrict — Split nucleotide sequence at restriction site. Updated to use Version 806 of REBASE, the Restriction Enzyme Database.
seqlogo — Display sequence logo for nucleotide or amino acid sequences. Updated to return a figure handle to the sequence logo.

Multiple Sequence Alignment Functions

Following is a new function:

multialignwrite — Write multiple alignment to file using ClustalW ALN format.

The following function is updated:

multialignread — Read multiple sequence alignment file. Updated to support PHYLIP (Phylogeny Inference Package) multiple sequence alignment files.

Gene Ontology Functions

The following function is updated:

goannotread — Read annotations from Gene Ontology annotated file. Updated to include two new properties, 'Fields' and 'Aspect', which let you read a subset of the data in the annotated file.

Protein Analysis Functions

Following are new functions:

cleavelookup — Find cleavage rule for enzyme or compound.
pdbsuperpose — Superpose 3-D structures of two proteins.
pdbtransform — Apply linear transformation to 3-D structure of molecule.

The following function is updated:

cleave — Cleave amino acid sequence with enzyme. Includes a new input argument that specifies the name of an enzyme or compound for which a cleavage rule is specified in the literature.

Mass Spectrometry Functions

Following are new functions:

mzcdf2peaks — Convert mzCDF structure to peak list.
mzcdfinfo — Return information about netCDF file containing mass spectrometry data.
mzcdfread — Read mass spectrometry data from netCDF file.
mzxmlinfo — Return information about mzXML file.

The following function is updated:

mzxmlread — Read data from mzXML file. Improved to read larger files, faster and without running out of memory. Updated with three new properties, 'Levels', 'TimeRange', and 'ScanIndices', which let you filter and read a subset of the data. Updated with a 'Verbose' property to control the progress display while reading the file.

Microarray File Format Functions

Following are new functions:

affygcrma — Perform GC Robust Multi-array Average (GCRMA) procedure on Affymetrix microarray probe-level data.
affyrma — Perform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data.
affysnpannotread — Read Affymetrix Mapping DNA array data from CSV-formatted annotation file.
geoseriesread — Read Gene Expression Omnibus (GEO) Series (GSE) format data.

The following functions are updated:

affyread — Read microarray data from Affymetrix GeneChip file. Updated so that Probes field in the return structure is now a single, which reduces memory usage.
celintensityread — Read probe intensities from Affymetrix CEL files. Updated so that PMIntensities and MMIntensities fields in the return structure are now singles, which reduces memory usage.
geosoftread — Read Gene Expression Omnibus (GEO) SOFT format data. Updated to support Platform (GPL) records.
getgeodata — Retrieve Gene Expression Omnibus (GEO) format data. Updated to support Platform (GPL) and Series (GSE) records.

Compatibility Considerations

Microarray Functions

Following are new functions:

affysnpintensitysplit — Split Affymetrix SNP probe intensity information for alleles A and B.
affygcrma — Perform GC Robust Multi-array Average (GCRMA) procedure on Affymetrix microarray probe-level data.
affyrma — Perform Robust Multi-array Average (RMA) procedure on Affymetrix microarray probe-level data.
DataMatrix — Create DataMatrix object.

The following functions are updated:

ilmnbslookup — Look up Illumina BeadStudio target (probe) sequence and annotation information. Updated to support BGX and TXT annotation files.
mattest — Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes. Updated to use unequal variance instead of equal variance for the test.
probesetlookup — Look up information for Affymetrix probe set. Updated to accept multiple probe set IDs/names or gene IDs.

Compatibility Considerations

In Bioinformatics Toolbox Version 3.1 and earlier, the mattest function used equal variance for the test. In Bioinformatics Toolbox Version 3.2, the mattest function uses unequal variance for the test.

DataMatrix Object

Following is a new object:

DataMatrix object — Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers.