Open AccessRecent improvements of the ProDom database of protein domain families
Author(s) -
F. Corpet,
Jérôme Gouzy,
Daniel Kahn
Publication year - 1999
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/27.1.263
Subject(s) - biology , web server , database , domain (mathematical analysis) , protein domain , phylogenetic tree , sequence database , genome , sequence alignment , zoom , interface (matter) , homology (biology) , computer science , genetics , world wide web , the internet , peptide sequence , gene , mathematical analysis , mathematics , paleontology , pulmonary surfactant , gibbs isotherm , biochemistry , lens (geology)
The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. The current version was built with a new improved procedure based on recursive PSI-BLAST homology searches. ProDom can be searched on the World Wide Web to study domain arrangements within either known families or new proteins, with the help of a user-friendly graphical interface (http://www.toulouse.inra.fr/prodom.html). Recent improvements to the ProDom server include: ProDom queries under the SRS Sequence Retrieval System; links to the PredictProtein server; phylogenetic trees and condensed multiple alignments for a better representation of large domain families, with zooming in and out capabilities. In addition, a similar server was set up to display the outcome of whole genome domain analysis as applied to 17 completed microbial genomes (http://www.toulouse.inra.fr/prodomCG.html ).
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