Bioinformatics Toolbox 3.4

Latest Features

Version 3.4

Released: 04 Sep 2009
 

Version 3.4, part of Release 2009b, includes the following enhancements:

• Expanded next-generation sequencing support, including optimized short-read sequence alignment and the reading and writing of common file formats, such as FASTQ and SFF files
• New objects for storing microarray experimental results and annotations
• New heatmap visualization object with annotation support
• Enhanced visualizations for unrooted phylogenetic trees and clustergrams
• New method for cluster validation of phylogenetic trees
• New function for calculating high-resolution isotopic mass distribution

See the Release Notes for details.

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Version 3.3

Released: 06 Mar 2009
 
Version 3.3, part of Release 2009a, includes the following enhancements:

• Expanded functionality of mass spectrometry functions for use with other bioanalytic separation techniques such as NMR, electrophoresis, chromatography, and spectroscopy
• Ability to read Illumina microRNA array annotation and data files
• New function to visualize results from microplate
• Expanded array comparative genomic hybridization (aCGH) analysis with heuristic stopping rule
• Expanded functionality for converting nucleotide sequences to amino acid sequences with support for ambiguous characters

See the Release Notes for details.

Version 3.2

Released: 09 Oct 2008
 

Version 3.2, part of Release 2008b, includes the following enhancements:

• Capability to contain microarray experiment data and metadata in one object
• New function to superpose 3-D protein structures
• New function to read and analyze GEO series format files
• Enhanced Robust Multiarray Average (RMA) and GC Robust Multiarray Average (GCRMA) analysis
• New functions for reading and analyzing Affymetrix® SNP Mapping arrays
• Enhanced performance when reading data from mzXML file
• New functions to read and write NetCDF mass spectrometry files

See the Release Notes for details.

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.

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.