| Version 3.2 (R2008b) Bioinformatics Toolbox™ Software Release Notes | |
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 | Printable Release Notes: PDF Current product documentation |
New and updated features in this version include:
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
probesetlookup — Look up information for Affymetrix probe set. Updated to accept multiple probe set IDs/names or gene IDs.
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.
There are many methods that let you create, index into, modify, create subsets, sort, perform operations on, analyze, and plot a DataMatrix object.
The Visualizing the Three-Dimensional Structure of a Molecule demo is updated to use the new pdbsuperpose function.
The following is a new sequence analysis demo:
Following are two new microarray data analysis demos:
The Exploring Gene Expression Data demo is updated to use the new DataMatrix object.
The Analyzing Affymetrix SNP Arrays for DNA Copy Number Variants demo is updated to use two new functions: affysnpannotread and affysnpintensitysplit.
The Preprocessing Affymetrix Microarray Data at the Probe Level demo is updated to use two new functions: affygcrma and affyrma.
| Bioinformatics Toolbox Release Notes | Version 3.1 (R2008a) Bioinformatics Toolbox Software | |
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