Recent improvements of the ProDom database of protein domain families

Authors: Corpet, Florence; Gouzy, Jérôme; Kahn, Daniel

Source: Nucleic Acids Research, Volume 27, Number 1, 01 January 1999 , pp. 263-267(5)

Publisher: Oxford University Press

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Abstract:

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 ).

Document Type: Research article

Affiliations: 1: Laboratoire de Biologie Moléculaire des Relations Plantes-Microoorganismes, INRA/CNRS, BP27, F-31326 Castanet-Tolosan cedex, France

Publication date: 1999-01-01

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Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.