Go to the abstract in the NAR 2000 Database Issue.
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L.B.M.R.P.M., U.M.R. 215, I.N.R.A.-C.N.R.S.
The ProDom database contains protein domain families automatically generated from the SWISS-PROT and TrEMBL databases by sequence comparisons. ProDom is built with the mkdom2 program, based on recursive PSI-BLAST homology searches. Inside each family, sequences are aligned using the Multalin program. ProDom-CG is built from ProDom as an extraction of sequences derived from complete genomes. Families found in ProDom-CG are thus a subset of the ProDom families. This allows for easy links between both databases. ProDom (rel. 2001.2) contains 339,763 sequences, among them 147,943 (44%) are kept for ProDom-CG (rel.CG42). ProDom can be searched on the World Wide Web to study domain arrangements for known protein families, with the help of a user-friendly graphical interface. The ESPript program is used to generate a publication quality alignment of ProDom families, including structural information. Blast and SRS requests can also be performed. Links are provided to the following protein or protein family databases: PDB, PROSITE, Pfam-A, InterPro.
ProDom construction: · A procedure has been developed to remove short linker sequences from ProDom. ProDom-CG: · ProDom-CG is now built as a subset of the current version of ProDom · Each family now has a stable accession number. The number is formed with the letters CG followed by the 6 digits already found in the corresponding ProDom family. Services: · The ESPript program is used to generate quality figures of the ProDom multialignments, including some structural information, when available (through links to PDB) · Links are now provided to the InterPro database.
Programme bioinformatique inter EPST (2000) European Union (QLRT-1999-30517)
Gouzy J., Corpet F. and Kahn D. (1996). Graphical interface for ProDom domain families, TIBS, 21:493
Gouzy J., Corpet F. & Kahn D. (1999). Whole genome protein domain analysis using a new method for domain clustering, Computers and Chemistry. 23:333-340
Corpet F., Servant F., Gouzy J. and Kahn D. (2000). ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons, Nucleid Acids Research. 28:267-269
Category Protein Sequence Motifs
Go to the abstract in the NAR 2000 Database Issue.