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ProDom


NAR Molecular Biology Database Collection entry number 214
Courcelle E., Beausse Y., CarrÈre S., Bru C., Dalmar S., Kahn D.
LIPM, UMR CNRS-INRA 2594/441, Toulouse, France

Database Description

The ProDom database contains protein domain families automatically generated from the SWISS-PROT and TrEMBL databases by sequence comparison. 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 ProDom families. ProDom (release 2003.1) contains 144,444 domain families containing two or more individual domains. 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 publication quality alignments of ProDom families, including structural information. BLAST and SRS requests can also be performed, with links to several other protein or protein family databases (PDB, PROSITE, Pfam-A and InterPro). ProDom-SG is a ProDom-based server dedicated to the selection of candidate domains which could show new types of folds for structural genomics projects.

Recent Developments

ProDom construction:
- The automatic clustering process is now initiated with the SCOP database.
- The norMD program is used as a tool for evaluation of the quality of alignments.
- ProDom-SG, a useful tool for structural genomics.

Graphical User Interface:
- ProDom domains can be displayed on 3D structures, when available.
- The Graphical User Interface was completely redesigned.

Acknowledgements

Programme bioinformatique inter EPST (2000-2002) European Union (QLRT-1999-30517)

References

1. Gouzy J., Corpet F. and Kahn D. (1996). Graphical interface for ProDom domain families, TIBS, 21:493
2. 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
3. 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


Go to the abstract in the NAR 2005 Database Issue.
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