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Avadis 3, GenBank 142.0, Phaser 1.2, InterPro 8.0, EcoCyc, MetaCyc, XML2PDB

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Strand Genomics has launched Avadis 3, an enterprise version of its microarray analysis software platform. The company said it also signed a licensing deal with Abgenix for Avadis 3, and that it had received around $1 million from India’s Technology Development Board for further development of the software.


GenBank release 142.0 is now available from NCBI at ftp://ftp.ncbi.nih.gov/. The release contains 40,325,321,348 base pairs and 35,532,003 entries, up by 1,335,978,783 base pairs and 1,855,785 sequence records (non-WGS) and 834,202,151 base pairs and 241,358 sequence records (WGS) from the April 141.0 release. Uncompressed, the 141.0 flat files require about 136 GB for the sequence files only. The ASN.1 version requires around 119 GB.


Phaser 1.2, a program for phasing macromolecular crystal structures with maximum likelihood methods, is available from the University of Cambridge at http://www-structmed.cimr.cam.ac.uk/phaser/.


InterPro 8.0 is available from the European Bioinformatics Institute at http://www.ebi.ac.uk/interpro/. The protein family database now contains 11,007 entries, representing 2,573 domains, 8,166 families, 201 repeats, 26 active sites, 21 binding sites, and 20 post-translational modifications. New features include an InterPro Domain Architecture viewer, extended 3D structure views, and increased taxonomy functionality.


SRI International has released version 8.1 of the EcoCyc E. coli model-organism database (http://ecocyc.org/), the MetaCyc metabolic pathway database (http://metacyc.org/), and pathway/genome databases for 16 additional organisms, (http://biocyc.org/), including a new database for Plasmodium falciparum.


The Fox Chase Cancer Center has released XML2PDB, an open-source file converter/parser in C++ for XML structure files from the Research Collaboratory for Structural Bioinformatics, at http://dunbrack.fccc.edu/xml2pdb.php. The program creates three files for use in homology modeling: a stripped-down PDB file that contains the title, the Seqres records for all chains, and coordinates of all atoms; a Fasta file with the one-letter code sequence of all proteins in the entry; and a file that contains records that provide the correspondence between Seqres numbering and coordinate residue numbering.

 

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