Bioinformatics Toolbox 2.0 Release Notes

Bioinformatics Toolbox 2.0 Release Notes

New Features

This section summarizes the new features and enhancements introduced in the Bioinformatics Toolbox 2.0.

Mass Spectrometry Data

New set of 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 — Non-parametric smoothing using Lowess method. mssgolay — Least-squares polynomial smoothing. msviewer — Plot a spectrum or a set of spectra.

Graph Visualization

New set of functions to view relationships between data with interactive maps.

biograph — 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.
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.

Protein Analysis

pdbplot — Plots 3D 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.

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. .

Known Software and Documentation Problems

Enhanced Features