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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.

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