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Melanie 4, Ensembl, Pfam, Artemis, ACT, Blast, Fasta

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Geneva Bioinformatics has released Melanie 4, the latest version of its 2D gel analysis software. New features include improved functionalities for viewing, analyzing, and reporting 2D gel data, as well as improved spot detection and spot matching algorithms, and new data management tools. A demo version of the software is available at www.genebio.com/melanie.

 

Version 11 of Ensembl, which has moved to a monthly update schedule, is now available at www.ensembl.org. The release contains new assemblies for human (NCBI build 31), rat (version 2.0 from Baylor College of Medicine), and Caenorhabditis elegans (WormBase release 95). The new release contains 24,847 genes for human, 21,276 genes for rat, and 19,537 genes for C. elegans.

 

Version 8.0 of the Pfam protein family database is available at www.sanger.ac.uk/Software/Pfam, http://pfam.wustl.edu, and www.cgr.ki.se/Pfam. Pfam 8.0 contains 5,193 protein families.

 

The Sanger Institute has released version 5 of Artemis, a DNA sequence viewer and annotation tool, at www.sanger.ac.uk/Software/Artemis/ v5/. According to the Artemis developers, there have been many bug fixes and improvements since the last release two years ago. Sanger has also made release 2 of ACT (Artemis Comparison Tool), a DNA sequence comparison viewer, available at www.sanger. ac.uk/Software/ACT/v2/. The new version is now able to compare more than two sequences.

 

The NCBI has released version 4 of its Blast databases, and announced that it will begin phasing out the Fasta versions of its Blast database files. As of May 5, 2003, the ftp directory at ftp://ftp.ncbi.nih.gov/ blast/db/ will contain only pre-formatted database files that correspond to the newest version of Blast (version 2.2.2). The NCBI warned that the new Blast database “may be incompatible with third-party programs which require Fasta sequences only.” Questions should be directed to: [email protected].

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