| Version 3.1 (R2008a) Bioinformatics Toolbox™ Software Release Notes | |
This table summarizes what's new in Version 3.1 (R2008a):
| New Features and Changes | Version Compatibility Considerations | Fixed Bugs and Known Problems | Related Documentation at Web Site |
|---|---|---|---|
| Yes Details below | Yes—Details labeled as Compatibility Considerations, below. See also Summary. | Bug
Reports Includes fixes | No |
New and updated features in this version include:
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.
fastawrite — Write to file using FASTA format. Updated such that if you specify an existing file, new data is appended to the file instead of overwriting it.
getgenbank — Retrieve sequence information from GenBank® database. Updated such that if you use the 'ToFile' property and specify an existing file, new data is appended to the file instead of overwriting it. Updated to allow you to access a partial sequence by adding new property 'PartialSeq'.
getgenpept — Retrieve sequence information from GenPept database. Updated such that if you use the 'ToFile' property and specify an existing file, new data is appended to the file instead of overwriting it. Updated to allow you to access a partial sequence by adding new property 'PartialSeq'.
getgeodata — Retrieve Gene Expression Omnibus (GEO) SOFT format data. Updated to retrieve both Sample (GSM) and Data Set (GDS) data.
In Bioinformatics Toolbox Version 3.0 and earlier, when writing to files using the fastawrite function or the getgenbank or getgenpept functions with the 'ToFile' property, if you specified an existing file, the file was overwritten. In Bioinformatics Toolbox Version 3.1, if you specify an existing file, new data is appended to the file instead of overwriting it.
The following functions are updated:
evalrasmolscript — Send RasMol script commands to Molecule Viewer window. Updated to use Version 11.4 of the Jmol molecule viewer.
molviewer — Display and manipulate 3-D molecule structure. 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 corresponding to torsion angles by creating an output structure.
rebasecuts — Find restriction enzymes that cut nucleotide sequence. Updated to use Version 710 of REBASE, the Restriction Enzyme Database.
restrict — Split nucleotide sequence at restriction site. Updated to use Version 710 of REBASE, the Restriction Enzyme Database.
The following functions are updated:
nwalign — Globally align two sequences using Needleman-Wunsch algorithm. Updated to improve pairwise sequence performance.
swalign — Locally align two sequences using Smith-Waterman algorithm. Updated to improve pairwise sequence performance.
The following function is updated:
dnds — Estimate synonymous and nonsynonymous substitution rates. Updated by adding 'AdjustStops' property to control whether stop codons are excluded from calculations.
The following functions are updated:
evalrasmolscript — Send RasMol script commands to Molecule Viewer window. Updated to use Version 11.4 of the Jmol molecule viewer.
molviewer — Display and manipulate 3-D molecule structure. 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.
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.
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.
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.
Replaced properties include:
'Dimension' — Replaced by the 'Cluster' property, which lets you cluster along the columns, rows, or both.
'Pdist' — Replaced by 'RowPdist' and 'ColumnPdist' properties.
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. Updated by adding 'BoxPlot' property, which lets you specify arguments to pass to the boxplot function, which creates the box plot.
mairplot — Create intensity versus ratio scatter plot of microarray data. Updated by adding 'PlotOnly' property, which lets you display the scatter plot without user interface components.
mattest — Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes. Updated by adding 'Bootstrap' property to run bootstrap tests.
mavolcanoplot — Create significance versus gene expression ratio (fold change) scatter plot of microarray data. Updated by adding 'PlotOnly' property, which lets you display the volcano plot without user interface components.
probesetvalues — Create table of Affymetrix probe set intensity values. Updated by adding 'Background' property to control the background correction.
zonebackadj — Perform background adjustment on Affymetrix microarray probe-level data using zone-based method. Updated to return a third output containing the estimated background values for each probe.
In Bioinformatics Toolbox Version 3.0 and earlier, the clustergram function included 'Dimension' and 'Pdist' properties. In Bioinformatics Toolbox Version 3.1, the 'Dimension' property is replaced by the 'Cluster' property, and the 'Pdist' property is replaced by the 'RowPdist' and 'ColumnPdist' properties.
Following is a new object:
clustergram object — Object containing hierarchical clustering analysis data.
The following are new methods of a clustergram object:
get — Retrieve information about clustergram object.
plot — Render clustergram heat map and dendrograms for clustergram object.
set — Set property of clustergram object.
view — View clustergram heat map and dendrograms for clustergram object.
The following is a new sequence analysis demo:
The following is a new microarray data analysis demo:
The following is a new visualization tool demo:
The Batch Processing of Spectra Using Distributed Computing demo is updated to use the latest features of the Parallel Computing Toolbox™ version 3.3, and is now called Batch Processing of Spectra Using Sequential and Parallel Computing
The Preprocessing Raw Mass Spectrometry Data demo is updated with state-of-the-art examples for peak detection using wavelets denoising, binning by hierarchical clustering, and binning by dynamic programming.
| Version 3.2 (R2008b) Bioinformatics Toolbox Software | Version 3.0 (R2007b) Bioinformatics Toolbox Software | |
| © 1984-2008- The MathWorks, Inc. - Site Help - Patents - Trademarks - Privacy Policy - Preventing Piracy - RSS |