The Cancer Genomics Group at the Whitehead Institute Center for Genome Research has released version 2.0 of its GeneCluster gene expression analysis application. The new release adds several features, including more options for pre-processing, marker selection, supervised classification, multiclass prediction, permutation test methods, and visualization.
GeneCluster 2.0 provides a gene marker selector based on neighborhood analysis, permutation tests, and visualization that allows users to view, sort, and color-code their data by keyword. It also includes tools for building supervised models using weighted voting and k-nearest neighbor algorithms. A beta version of the software, which can also be used for proteomic data, is available for free at www.genome.wi.mit.edu/cancer/software/software.html.
A beta version of eGenome — a position-based catalog of transcripts, markers, polymorphisms, large-insert clones, and DNA sequences for the human genome — is available from the Children’s Hospital of Philadelphia at http://egenome.chop.edu. A stable site with up-to-date content is expected to launch in July.
SciQuest of Research Triangle Park, NC, has released version 2.5 of its Gene Construction Kit, a DNA manipulation, cloning design, and illustration tool.
Enhancements in version 2.5 include a deluxe importer module that allows users to import GenBank and EMBL data and a customizable interface that converts GenBank and EMBL features to graphical GCK features. The software has also been ported to Mac OS X.
An IPI (International Protein Index) set is now available for mouse from the European Bioinformatics Institute at ftp://ftp.ebi.ac.uk/pub/databases/IPI/current.
The mouse IPI is a non-redundant protein set assembled from mouse sequences in Ensembl, SwissProt, Trembl, and RefSeq. Version 1.0 of the mouse IPI contains 30,517 sequences.