The BioInformer nr. 2, 1997 -- ProDom 34




	A publication of EMBL - Outstation Hinxton, The European Bioinformatics Institute


		ProDom release 34 Introduction The Protein Domain database, ProDom, release 34, has been constructed by clustering homologous segments derived from 53145 non-fragmentary sequences present in SWISS-PROT 34. It provides 18086 mutiple alignments and consensus sequences for homologous domain families. The vast majority of these families have been generated automatically using MKDOM, a much improved version of the DOMAINER program (Sonnhammer & Kahn, 1994, Protein Science, 3:482-492; Gouzy, Eugene, Greene, Kahn & Corpet, in preparation). Several steps have been taken towards improving the quality of ProDom. In particular, all multiple alignments have been recalculated ab initio using the MultAlin program (Corpet, 1988, Nucl. Acids Res. 16:10881-10890). In addition a new expertise procedure has been introduced to validate some domain boundaries. Release notes The Web user interface has also been considerably enhanced. Links are provided to and from PROSITE and PDB. They have been calculated with the help of the LASSAP program. Domain families can be searched by keyword, and graphical representations of domain arrangements can considerably facilitate the structural interpretation of large protein families. In addition, a sensitive homology search procedure is now provided which scans all domain sequences in ProDom and retrieves matches with only one sequence for each domain family, thus drastically reducing output redundancy. The most significant matches are visualised graphically to assist with interpretation. For long queries the former less sensitive but faster search on consensus sequences is also provided. Choice is given between the classical NCBI BLAST 1.4.9 and the new WU-BLAST 2.0a8 allowing for gapped outputs. Availability The Protein Domain Database release can be retrieved in full by FTP or can be queried at the Prodom server. Information supplied by: Daniel Kahn Resources and further information National Institute of Agricultural Agricultural Research (INRA) http://www.inra.fr/ENG/index.html ProDom WWW server http://protein.toulouse.inra.fr/prodom.html ProDom 34 release database ftp://ftp.toulouse.inra.fr/pub/prodom/prodom34 For more info e-mail: proquest@toulouse.inra.fr MultiAlin program http://www.toulouse.inra.fr/multalin.html LASSAP program http://alize.inria.fr/ Washington University BLAST archives http://blast.wustl.edu/ External sites are not endorsed by EMBL-EBI

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