User manual MATLAB BIOINFORMATICS TOOLBOX RELEASE NOTE

[. . . ] Bioinformatics ToolboxTM Release Notes How to Contact The MathWorks Web Newsgroup www. mathworks. com/contact_TS. html Technical Support www. mathworks. com comp. soft-sys. matlab suggest@mathworks. com bugs@mathworks. com doc@mathworks. com service@mathworks. com info@mathworks. com Product enhancement suggestions Bug reports Documentation error reports Order status, license renewals, passcodes Sales, pricing, and general information 508-647-7000 (Phone) 508-647-7001 (Fax) The MathWorks, Inc. 3 Apple Hill Drive Natick, MA 01760-2098 For contact information about worldwide offices, see the MathWorks Web site. Bioinformatics ToolboxTM Release Notes © COPYRIGHT 2003­2010 by The MathWorks, Inc. The software described in this document is furnished under a license agreement. The software may be used or copied only under the terms of the license agreement. [. . . ] Updated to use Version 11. 4 of the Jmol molecule viewer. · ramachandran -- Draw Ramachandran plot for Protein Data Bank (PDB) data. Updated to handle PDB files with multiple chains and models by adding three properties: 'Chain', 'Plot', and 'Model'. Updated Ramachandran plot to mark glycine residues and display reference regions by adding three properties: 'Glycine', 'Regions', and 'RegionDef'. Updated Ramachandran plot to display amino acid information in ToolTip. Updated to easily determine the names and sequence positions of amino acids by creating an output structure. Microarray File Format Functions Following is a new function: · ilmnbsread -- Read microarray data exported from Illumina BeadStudio software. The following functions are updated: · celintensityread -- Read probe intensities from Affymetrix CEL files. Updated output structure to include a new field, GroupNumbers, which contains group numbers of probes. · getgeodata -- Retrieve Gene Expression Omnibus (GEO) SOFT format data. Updated to retrieve both Sample (GSM) and Data Set (GDS) data. Microarray Functions Following are new functions: · affysnpquartets -- Create table of SNP probe quartet results for Affymetrix probe set. · cghfreqplot -- Display frequency of DNA copy number alterations across multiple samples. · ilmnbslookup -- Look up Illumina BeadStudio target (probe) sequence and annotation information. · redbluecmap -- Create red and blue color map. 30 Version 3. 1 (R2008a) Bioinformatics ToolboxTM Software The following functions are updated: · clustergram -- Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object. Updated properties include: - 'Linkage' -- Can specify linkage method separately for rows and columns. 'Dendrogram' -- Can specify color threshold separately for rows and columns. 'Dimension' -- Replaced by the 'Cluster' property, which lets you cluster along the columns, rows, or both. 'Pdist' -- Replaced by 'RowPdist' and 'ColumnPdist' properties. Replaced properties include: New properties include: 'Standardize' -- Specifies the dimension for standardizing the data. 'DisplayRange' -- Specifies the display range of standardized values. 'LogTrans' -- Controls the log2 transform of the data. 'Impute' -- Specifies a function and properties to impute missing data. 'RowMarker' -- Adds color and text marker to a group of rows. 'ColumnMarker' -- Adds color and text marker to a group of columns. The interactivity of the clustergram figure is enhanced with the following features: Select a group of rows or columns and display the group number and genes or samples within. Create a new clustergram of only a group of the data. Export data as a clustergram object or structure in the MATLAB Workspace. · maboxplot -- Create box plot for microarray data. [. . . ] · gprread -- Read microarray data from GenePix® Results (GPR) files. · mapcaplot -- Create a Principal Component plot of expression profile data. · clustergram -- Updated function to do two way bi-clustering. Protein Analysis Function isoelectric -- Estimate the isoelectric point (the pH at which the protein has a net charge of zero) for an amino acid sequence and estimate the charge for a given pH. Sequence Alignment Functions · seqdisp -- Formats sequence output for easy viewing. · seqmatch -- Find matches for every string in a library. [. . . ]