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Version 2.0 (R14SP1+) Bioinformatics Toolbox Software

This table summarizes what's new in Version 2.0 (Release 14SP1+):

New Features and Changes	Version Compatibility Considerations	Fixed Bugs and Known Problems	Related Documentation at Web Site
Yes Details below	No	No bug fixes	No

New features and changes introduced in this version are

• Mass Spectrometry Data Analysis

• Graph Visualization Object and Methods

• Statistical Learning

• Sequence Analysis

• Protein Analysis

• Microarray Analysis

• Updated Web Connectivity Function

Mass Spectrometry Data Analysis

Following are new functions designed for preprocessing and classification of raw mass spectrometry data from SELDI-TOF and MALDI-TOF spectrometers.

• msresample — Resample with antialias filtering.

• msbackadj — Correct a baseline by estimation.

• msalign — Align a spectrum to a set of candidate peaks.

• msheatmap — Draw a heat map image for a set of spectra and check alignments.

• msnorm — Normalize a set of spectra.

• mslowess — Nonparametric smoothing using the Lowess method.

• mssgolay — Least-squares polynomial smoothing.

• msviewer — Plot a spectrum or a set of spectra.

Graph Visualization Object and Methods

New object and set of methods to view relationships between data with interactive maps.

• biograph — Function to create a biograph object.

• dolayout — Calculate node and edge positions.

• getnodesbyid — Get handles to nodes.

• getedgesbynodeid — Get handles to edges.

• view — Render a graph in its viewer.

• getancestors — Find ancestors.

• getdescendants — Find descendants.

• getrelatives — Find neighbors.

Statistical Learning

New set of functions to classify data and identify features in the data.

• classperf — Evaluate the performance of a classifier.

• crossvalind — Cross-validation index generation.

• knnclassify — K-Nearest neighbor classifier.

• knnimpute — Impute missing data using the nearest neighbor method.

• randfeatures — Randomized subset feature selection.

• sqtlfeatures — Sequential forward feature selection. This function will be renamed to rankfeatures in Version 2.1.

• svmclassify — Classify using a support vector machine classifier.

• svmtrain — Train a support vector machine classifier.

Sequence Analysis

New functions for analysis and visualization of multiple sequences.

• seqconsensus — Computes the consensus sequence for a set of sequences.

• seqlogo — Displays sequence logos for DNA and protein sequences.

• seqprofile — Computes the sequence profile of a multiple alignment.

Updated functions.

• palindromes — Updated to allow for gaps in the palindrome.

• seqshoworfs, seqshowwords, showalignment — Updated to display the results in a Figure window. (This may cause problems on the Mac^®.)

In Bioinformatics Toolbox 2.0 the functions seqlogo, seqshowwords, seqshoworfs, and showalignment use Java™ based figures. Currently on the Macintosh^®, Java figures are not enabled by default. If you use these functions on a Macintosh, you should start the MATLAB software with

 matlab -useJavaFigures

Protein Analysis

• pdbplot — Plots 3-D backbone structure of proteins in a PDB file.

Microarray Analysis

• quantilenorm — Quantile normalization.

New set of functions for working with Affymetrix GeneChip data sets.

• probelibraryinfo — Get library information for a probe.

• probesetlink — Show probe set information from NetAffx™.

• probesetlookup — Get gene information for a probe set.

• probesetplot — Plot probe set values.

• probesetvalues — Get probe set values from CEL and CDF information.

• manorm — Normalization by scaling and centering replaces the functions mamadnorm and mameannorm.

• affyread — Updated with output structures that have changed slightly. Some redundant fields have been removed from CDF and CHP structure. GIN database files are now supported. Version 4 of the Affymetrix GDAC File Access Runtime Libraries is provided.

Note   If you use mamadnorm or mameannorm in any of your personal M-files, please update your files with the new function manorm. These functions are now obsolete and may be removed from future releases of the Bioinformatics Toolbox software.

• geosoftread — Updated with supports Gene Expression Omnibus Database records (GDS files).

• maimage — Updated with supports Affymetrix CEL data.

• maboxplot — Now supports Affymetrix CHP data.

Updated Web Connectivity Function

getgenbank — Now returns CDS information for a gene in a structure allowing direct access to the transcribed sequence.

Version 2.0.1 (R14SP2) Bioinformatics Toolbox Software

Version 1.1.1 (R14SP1) Bioinformatics Toolbox Software

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