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Koadarray 2.4, MAS5, Integrated Genome Browser, caWorkbench 2.0, UCSC Genome Browser, Ensembl, ROCS 2.1, EON 1.1, Fgenesh

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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.

Filed under

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.