Bioinformatics Toolbox™ 3.1

Latest Features

Version 3.1

Released: 01 Mar 2008
 

Version 3.1, part of Release 2008a, includes the following enhancements:

• Illumina® BeadStudio microarray data support
• Expanded clustergram feature with more flexible clustering analysis and additional annotation and export functionality
• Expanded Ramachandran plotting with more accessible residue information and ability to display reference regions and plot multiple chains and models
• Expanded array comparative genomic hybridization (aCGH) visualization with frequency plot
• Gene Expression Omnibus (GEO) SOFT data support expanded to allow the retrieval of Data Set (GDS) data
• Improved performance of pairwise sequence alignment
• New demo on analyzing metagenomic data

See the Release Notes for details.

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Version 3.0

Released: 01 Sep 2007
 

Version 3.0, part of Release 2007b, includes the following enhancements:

• Array comparative genomic hybridization (aCGH) analysis and visualization
• RNA secondary structure prediction and visualization
• BLAST reports from local databases
• Graph clustering
• Common motifs searching

See the Release Notes for details.

Version 2.6

Released: 19 Apr 2007
 

Version 2.6, an update to Release 2007a, includes the following enhancements:

• Enhanced support for reading Affymetrix files from expression, genotyping (SNP), or resequencing assays on all platforms, except Solaris
• Ability to perform background adjustment on Affymetrix microarray probe-level data using zone-based method
• New function for aligning two data sets containing sequential observations
• New demos for mass spectrometry functionality

See the Release Notes for details.

Version 2.5

Released: 01 Mar 2007
 

• Support for analysis of LCMS and GCMS data
• Ability to perform GCRMA background adjustment, quantile normalization, and RMA summarization of Affymetrix microarray probe-level data
• Ability to estimate false discovery rate (FDR) of differentially expressed genes
• Ability to display and manipulate 3-D molecule structures
• Expanded support vector machine classifier function
• Enhanced control of the phylogenetic tree display

See the Release Notes for details.

Version 2.4

Released: 01 Sep 2006
 
Version 2.4, part of Release 2006b, includes the following enhancements:

• New functions to parse annotated sequence data and read mzXML files
• New functions to apply basic graph theory algorithms to sparse matrices and biograph objects
• Updated functions to read and access data
• Updated functions to analyze and visualize microarray data
• Updated functions to align and visualize sequences

See the Release Notes for details.

Version 2.3

Released: 04 May 2006
 
Version 2.3, an update to Release 2006a, includes the following enhancements:

• Draw linear or circular map of features from a GenBank structure
• Calculate gene expression values from Affymetrix probe-level data using robust multi-array average (RMA)
• Perform background adjustment on Affymetrix probe-level data using RMA
• Perform rank-invariant set normalization
• Create a volcano plot of microarray data
• Perform two-sample, two-tailed t-test to evaluate differential expression of genes from two experimental conditions or phenotypes

See the Release Notes for details.

Version 2.2.1

Released: 01 Mar 2006
 

Version 2.2.1, part of Release 2006a, includes a number of bug fixes. See the Release Notes for details.

Version 2.2

Released: 17 Nov 2005
 

• An interactive viewer for multiple sequence analysis
• Functionality for working with gene ontology data
• Additional microarray file format support
• Demo on working with whole genome data using memory mapping

See the Release Notes for details.

Version 2.1.1

Released: 01 Sep 2005
 

Version 2.1.1, part of Release 14 with Service Pack 3, includes a number of bug fixes. See the Release Notes for details.

Version 2.1

Released: 26 May 2005
 

• Progressive multiple sequence alignment with support for distributed computing
• Neighbor-joining phylogenetic reconstruction
• Enhanced phylogenetic tree handling tools, such as weighting, canonical forms, and rerooting
• Interactive sequence viewer for viewing features such as CDs and ORFs

See the Release Notes for details.

Version 2.0.1

Released: 07 Mar 2005
 

Version 2.0.1, part of Release 14 with Service Pack 2, includes bug fixes. See the Release Notes for details.

Version 2

Released: 18 Nov 2004
 

• Preprocessing and analysis functionality for SELDI/MALDI mass spectrometry data
• Visualization tool for viewing interaction graphs
• Machine learning functions for classification and pattern recognition
• Enhanced microarray normalization tools
• Additional sequence visualization and analysis tools

Version 1.1.1

Released: 22 Sep 2004
 

Version 1.1.1 includes bug fixes.

Version 1.1

Released: 02 Jun 2004
 

• Supports genomic, proteomic, and gene expression file formats
• Provides Internet database access
• Enables genomic and proteomic sequence alignment
• Enables genomic and proteomic sequence statistics, conversion, and manipulation
• Supports microarray data normalization and visualization
• Provides phylogenetic tree analysis

Version 1.0.1

Released: 06 Nov 2003
 

Version 1.0.1 of the Bioinformatics Toolbox contains minor enhancements.