Version 2.4 (R2006b) Bioinformatics Toolbox™ Software Release Notes

Version 2.4 (R2006b) Bioinformatics Toolbox Software

This table summarizes what's new in Version 2.4 (Release 2006b):

New functions, obsoleted functions, and changes introduced in this version are

• Data Formats and Database Functions

• Sequence Utilities Functions

• Sequence Visualization Functions

• Multiple Sequence Alignment Functions

• Microarray File Formats

• Microarray Data Analysis and Visualization Functions

• Graph Theory Functions

• Graph Visualization Methods

• Phylogenetic Tree Methods

Data Formats and Database Functions

Following is a new function for getting data into the MATLAB environment:

• mzxmlread — Read mzXML file into the MATLAB software as structure.

The following functions were updated:

• celintensityread — Read probe intensities from Affymetrix CEL files (Windows 32). Updated to include a new property, Verbose, which controls the display of a progress report showing the name of each CEL file as it is read.

• fastaread — Read data from FASTA file. Updated to include a new property, Blockread, which controls reading a single entry or block of entries from a file.

• geosoftread — Read Gene Expression Omnibus (GEO) SOFT format data. Updated to read Data Set (GDS) files as well as Sample (GSM) files.

• getblast — BLAST report from NCBI Web site. Updated to include a new property, WaitTilReady, which pauses the MATLAB software and waits a specified time (minutes) for a report from the NCBI Web site.

• scfread — Read trace data from SCF file. Updated to include more output options.

Sequence Utilities Functions

Following is a new function for parsing sequence data:

• featuresparse — Parse features from GenBank, GenPept, or EMBL data.

Sequence Visualization Functions

The following function was updated:

• seqtool — Open tool to interactively explore biological sequences. Updated to download sequences from the EMBL database, interactively move the viewing frame in the Sequence Viewer by pressing and holding Ctrl while click-dragging, and export an amino acid translation as a FASTA file or to the MATLAB Workspace.

Multiple Sequence Alignment Functions

The following function was updated:

• multialignviewer — Open viewer for multiple sequence alignments. Updated to export consensus sequences.

Microarray File Formats

The following function was updated:

• celintensityread — Read probe intensities from Affymetrix CEL files (Windows 32). Updated to include a new property, Verbose, which controls the display of a progress report showing the name of each CEL file as it is read.

Microarray Data Analysis and Visualization Functions

The following functions were updated:

• clustergram — Create dendrogram and heat map. Updated to include a new property, OptimalLeafOrder, which enables or disables the optimal leaf ordering calculation, which determines the leaf order that maximizes the similarity between neighboring leaves.

• mairplot — Create intensity versus ratio scatter plot for microarray signals. Updated to include a new property, Type, which creates either an IR plot or MA plot, changing the plot axes to log scale, and adding plot interactive features such as displaying gene labels, changing factor lines, normalizing data, and exporting data.

• mapcaplot — Create Principal Component plot of expression profile data. Updated by adding an export feature.

• redgreencmap — Create red and green colormap. Updated to include a new property, Interpolation, which sets the method for color interpolation.

Graph Theory Functions

Following are new functions for applying basic graph theory algorithms to sparse matrices:

• graphallshortestpaths — Find all shortest paths in graph.

• graphconncomp — Find strongly or weakly connected components in graph.

• graphisdag — Test for cycles in directed graph.

• graphisomorphism — Find isomorphism between two graphs.

• graphisspantree — Determine if tree is spanning tree.

• graphmaxflow — Calculate maximum flow and minimum cut in directed graph.

• graphminspantree — Find minimal spanning tree in graph.

• graphpred2path — Convert predecessor indices to paths.

• graphshortestpath — Solve shortest path problem in graph.

• graphtopoorder — Perform topological sort of directed acyclic graph.

• graphtraverse — Traverse graph by following adjacent nodes.

Graph Visualization Methods

Following are new methods for applying basic graph theory algorithms to a biograph object:

• allshortestpaths — Find all shortest paths in biograph object.

• conncomp — Find strongly or weakly connected components in biograph object.

• getmatrix — Get connection matrix from biograph object.

• isdag — Test for cycles in biograph object.

• isomorphism — Find isomorphism between two biograph objects.

• isspantree — Determine if tree created from biograph object is spanning tree.

• maxflow — Calculate maximum flow and minimum cut in biograph object.

• minspantree — Find minimal spanning tree in biograph object.

• shortestpath — Solve shortest path problem in biograph object.

• topoorder — Perform topological sort of directed acyclic graph extracted from biograph object.

• traverse — Traverse biograph object by following adjacent nodes.

Phylogenetic Tree Methods

Following is a new method for the phytree object:

• getmatrix — Convert phytree object into a relationship matrix.

Version 2.5 (R2007a) Bioinformatics Toolbox Software

Version 2.3 (R2006a+) Bioinformatics Toolbox Software