Version 2.0 (R14SP1+) Bioinformatics Toolbox™ Software Release Notes

Version 2.0 (R14SP1+) Bioinformatics Toolbox™ Software

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

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