ProDom: automated clustering of homologous domains

Florence Servant; Catherine Bru; Sébastien Carrère; Emmanuel Courcelle; Jérĵme Gouzy; David Peyruc; Daniel Kahn

doi:10.1093/bib/3.3.246

ProDom: automated clustering of homologous domains

Brief Bioinform. 2002 Sep;3(3):246-51. doi: 10.1093/bib/3.3.246.

Authors

Florence Servant¹, Catherine Bru, Sébastien Carrère, Emmanuel Courcelle, Jérĵme Gouzy, David Peyruc, Daniel Kahn

Affiliation

¹ SWISSPROT Group, EBI.

PMID: 12230033
DOI: 10.1093/bib/3.3.246

Abstract

The ProDom database is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases. An associated database, ProDom-CG, has been derived as a restriction of ProDom to completely sequenced genomes. The ProDom construction method is based on iterative PSI-BLAST searches and multiple alignments are generated for each domain family. The ProDom web server provides the user with a set of tools to visualise multiple alignments, phylogenetic trees and domain architectures of proteins, as well as a BLAST-based server to analyse new sequences for homologous domains. The comprehensive nature of ProDom makes it particularly useful to help sustain the growth of InterPro.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Protein*
Genome
Information Services
Internet
Models, Molecular
Phylogeny
Protein Structure, Tertiary*
Proteins / chemistry*
Proteins / classification
Sequence Alignment
Sequence Analysis, Protein
User-Computer Interface

Substances

Proteins