Koada Technology has released Koadarray 2.4, a software program for automated analysis and quantification of array images. Koada said that the software enables automatic spot finding without the requirement to define spot or grid dimensions. In addition, Koadarray 2.4 includes an improved spot confidence index, unattended multiple image analyses, and configurable text data output. A free 30-day evaluation version is available at http://www.koadarray.com/.
Affymetrix has released the C++ source code for its MAS5 statistical algorithm under the GNU GPL at http://www.affymetrix.com/support/developer/stat_sdk/index.affx. The company has also released a new version of its Integrated Genome Browser (http://www.affymetrix.com/support/developer/tools/igbsource_terms.affx).
Columbia University has released caWorkbench 2.0, an integrative genomics package that contains modules for microarray analysis, database searching, pattern recognition, and promoter analysis, at http://amdec-bioinfo.cu-genome.org/html/caWorkBench.htm.
The University of California Santa Cruz Genome Bioinformatics Group has made the D. melanogaster release 4 assembly available via the UCSC Genome Browser at http://genome.ucsc.edu/cgi-bin/hgTracks?db=dm2. This version includes Release 4 euchromatic sequence from the Berkeley Drosophila Genome Project, Release 3.2 heterochromatic genome sequence from the Drosophila Heterochromatin Genome Project, and Release 4.0 annotations from FlyBase.
Ensembl has released a preliminary site for the 3.4 (November 2004) rat assembly at http://pre.ensembl.org/Rattus_norvegicus/. Rodent proteins and cDNAs have been mapped to the genome, which is searchable using Blast and SSAHA.
OpenEye Scientific Software has released ROCS 2.1 and EON 1.1. ROCS rapidly aligns molecules and compares their 3D shapes, while EON compares electrostatic potential fields throughout space around molecules.
Softberry has released new Fgenesh gene-finding parameters for chicken and Xenopus genome annotation at http://www.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind.