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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


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

Affymetrix has released the C++ source code for its MAS5 statistical algorithm under the GNU GPL at The company has also released a new version of its Integrated Genome Browser (

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

The University of California Santa Cruz Genome Bioinformatics Group has made the D. melanogaster release 4 assembly available via the UCSC Genome Browser at 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 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

Filed under

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.