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GeneData, European Bioinformatics Institute, Ensembl, National Center for Biotechnology Information


GeneData, headquartered in Basel, Switzerland, has released two new modules for its GeneData Screener system for the analysis of high-throughput screening data. The first module, Screener Condenser, performs data standardization and annotation. The second, Screener Analyst, conducts cross-assay compound profiling based on HTS data.

Release 5.3 of the InterPro integrated database of protein domains, families, and functional sites, is available from the European Bioinformatics Institute at The current release was built from Pfam 7.7, Prints 33.0, Prosite 17.25, ProDom 2001.3, Smart 3.4, TIGRfams 2.1, and the current Swiss-Prot and Trembl data. It contains 6,725 entries, representing 1,453 domains, 5,121 families, 136 repeats, and 15 post-translational modification sites. Overall, there are 2,932,939 InterPro hits from 850,953 Swiss-Prot and Trembl protein sequences. The sixth production release of InterPro is scheduled for March 2003. For Release 6.0, the InterPro developers plan to integrate more databases and include links to Protein Information Resource superfamilies.

The first assembly of the rat genome is now available through Ensembl at Ensembl Rat release 9.1.1 contains data from the first data release of the international rat genome project, which announced the completion of its draft assembly last week (see brief, p. 8). Ensembl currently offers the ability to search the rat assembly by Blast and SSAHA. An annotated assembly of the rat genome, performed in cooperation with the Rat Genome Database ( is expected in the first quarter of 2003. The rat data can also be downloaded directly from Baylor College of Medicine at

The National Center for Biotechnology Information has released a new NCBI Toolbox and Blast binaries 2.2.5 for Standalone Blast. Binaries are located at the NCBI FTP site: The NCBI Toolbox, which contains the Blast source code, is available at:

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