Version 2.5 (R2007a) Bioinformatics Toolbox Software :: Bioinformatics Toolbox Release Notes (Bioinformatics Toolbox)

Version 2.5 (R2007a) Bioinformatics Toolbox Software

This table summarizes what's new in Version 2.5 (Release 2007a):

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, updated, and deprecated functions in this version include:

Data Formats and Database Functions

Following are new functions for reading and creating files:

affyprobeseqread — Read data file containing probe sequence information for Affymetrix GeneChip array.
pdbwrite — Write to file using Protein Data Bank (PDB) format.

The following functions were updated:

celintensityread — Read probe intensities from Affymetrix CEL files (Windows^® 32). Updated so that the order of columns (CEL files) in return matrices PMIntensities and MMIntensities matches the order of CEL files in the CELFiles input argument.
pdbread — Read data from Protein Data Bank (PDB) file. Updated so that the six fields containing coordinate information (Atom, AtomSD, AnisotropicTemp, AnisotropicTempSD, Terminal, and HeterogenAtom) are now subfields within the Model field of the MATLAB structure. Updated to include a new property, ModelNum, which reads only the specified model from a PDB-formatted text file.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.4 and earlier, the celintensityread function ordered the columns (CEL files) of return matrices PMIntensities and MMIntensities alphabetically.

In Bioinformatics Toolbox Version 2.4 and earlier, the pdbread function stored coordinate information in six fields (Atom, AtomSD, AnisotropicTemp, AnisotropicTempSD, Terminal, and HeterogenAtom) within the MATLAB structure. These six fields are now subfields within the Model field of the MATLAB structure.

Demo for Data Formats and Database Functions

The Accessing NCBI Entrez Databases with E-Utilities demo illustrates how to programatically search and retrieve data.

Statistical Learning Functions

Following are new functions:

optimalleaforder — Determine optimal leaf ordering for hierarchical binary cluster tree.
svmsmoset — Create or edit Sequential Minimal Optimization (SMO) options structure.

The following function was updated:

svmtrain — Train support vector machine classifier. Updated to include a new SMO method and a new property, SMO_Opts, which provides options for the SMO method. The BoxConstraint property has changed, including a new default value.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.4 and earlier, the svmtrain function used a BoxConstraint property with a default of . In Bioinformatics Toolbox Version 2.5, the default is 1, which can lead to slightly different results.

Protein Analysis and Sequence Utilities Functions

Following are new functions:

evalrasmolscript — Send RasMol script commands to molecule viewer.
molviewer — Display and manipulate 3-D molecule structure.
proteinpropplot — Plot properties of amino acid sequence.
seqinsertgaps — Insert gaps into nucleotide or amino acid sequence.

The following functions were updated:

featuresparse — Parse features from GenBank, GenPept, or EMBL data. Updated to include a new property, Sequence, which controls the extraction, when possible, of the sequences.
oligoprop — Calculate sequence properties of DNA oligonucleotide. Updated to handle ambiguous N characters in a sequence.

The following function is obsolete:

pdbplot — Plot 3-D protein structure. This function was replaced by the molviewer function.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.5, the pdbplot function was replaced by the molviewer function. If you have any scripts that call the pdbplot function, you need to update them to call the molviewer function.

Demo for Protein Analysis and Sequence Utilities Functions

The Visualizing the Three-dimensional Structure of a Molecule demo illustrates the molviewer function.

Sequence Alignment Functions

The following function was updated:

seqpdist — Calculate pairwise distance between sequences. Updated to assume that all input sequences are aligned if they have the same length, regardless of the presence of gaps. If you know your input sequences are not aligned, you can align them before passing them to seqpdist (for example, using multialign), or set PairwiseAlignment to true when using seqpdist.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.4 and earlier, the seqpdist function assumed all input sequences were aligned if they had the same length and at least one gap.

Demo for Sequence Alignment Functions

The Comparing Whole Genomes demo illustrates how to compare features of organisms on a genomic evolution scale.

Microarray File Formats Functions

Following is a new function:

affyprobeseqread — Read data file containing probe sequence information for Affymetrix GeneChip array.

The following function was updated:

celintensityread — Read probe intensities from Affymetrix CEL files (Windows 32). Updated so that the order of columns (CEL files) in return matrices PMIntensities and MMIntensities matches the order of CEL files in the CELFiles input argument.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.4 and earlier, the celintensityread function ordered the columns (CEL files) of return matrices PMIntensities and MMIntensities alphabetically.

Microarray Normalization and Filtering Functions

Following are new functions:

affyprobeaffinities — Compute Affymetrix probe affinities from their sequences and MM probe intensities.
gcrmabackadj — Perform GC Robust Multi-array Average (GCRMA) background adjustment on Affymetrix microarray probe-level data using sequence information.
gcrma — Perform GC Robust Multi-array Average (GCRMA) background adjustment, quantile normalization, and median-polish summarization on Affymetrix microarray probe-level data.

Demo for Microarray File Formats, Normalization, and Filtering Functions

The Preprocessing Affymetrix Microarray Data at the Probe Level demo illustrates the affyprobeseqread, affyprobeaffinities, gcrmabackadj, and gcrma functions.

Microarray Data Analysis and Visualization Functions

Following is a new function:

mafdr — Estimate false discovery rate (FDR) of differentially expressed genes from two experimental conditions or phenotypes.

The following function was updated:

mattest — Perform two-tailed t-test to evaluate differential expression of genes from two experimental conditions or phenotypes. Updated to include a new property, Permute, which controls whether permutation tests are run.

Demo for Microarray Data Analysis and Visualization Functions

The Exploring Gene Expression Data demo illustrates the mattest and mafdr functions.

Mass Spectrometry Functions

Following are new functions:

msdotplot — Plot set of peak lists from LC/MS or GC/MS data set.
mspalign — Align mass spectra from multiple peak lists from LC/MS or GC/MS data set.
mspeaks — Convert raw mass spectrometry data to peak list (centroided data).
msppresample — Resample mass spectrometry signal while preserving peaks.
mzxml2peaks — Convert mzXML structure to peak list.

The following function was updated:

msheatmap — Create pseudocolor image of set of mass spectra. Updated to handle LC/MS and GC/MS data.

Phylogenetic Tree Tools Functions

Following is a new function:

seqinsertgaps — Insert gaps into nucleotide or amino acid sequence.

The following functions were updated:

dnds — Estimate synonymous and nonsynonymous substitution rates. Updated to include two new properties, Verbose, which controls the display of the codons considered in the computations and their amino acid translations, and Window, which performs the calculations over a sliding window.
dndsml — Estimate synonymous and nonsynonymous substitution rates using maximum likelihood method. Updated to include a new property, Verbose, which controls the display of the codons considered in the computations and their amino acid translations.
seqpdist — Calculate pairwise distance between sequences. Updated to assume that all input sequences are aligned if they have the same length, regardless of the presence of gaps. If you know your input sequences are not aligned, you can align them before passing them to seqpdist (for example, using multialign), or set PairwiseAlignment to true when using seqpdist.

Compatibility Considerations

In Bioinformatics Toolbox Version 2.4 and earlier, the seqpdist function assumed all input sequences were aligned if they had the same length and at least one gap.