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PMID: 9016538 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Novel developments with the PRINTS protein fingerprint database.

Nucleic acids research ·Vol. 25 ·No. 1 ·1997-01-01 ·Pages 212-7

Attwood TK, Beck ME, Bleasby AJ, Degtyarenko K, Michie AD, Parry-Smith DJ

Abstract

The PRINTS database of protein family 'fingerprints' is a diagnostic resource that complements the PROSITE dictionary of sites and patterns. Unlike regular expressions, fingerprints exploit groups of conserved motifs within sequence alignments to build characteristic signatures of family membership. Thus fingerprints inherently offer improved diagnostic reliability by virtue of the mutual context provided by motif neighbours. To date, 600 fingerprints have been constructed and stored in PRINTS, representing a 50% increase in the size of the database in the last year. The current version, 13.0, encodes approximately 3000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is accessible via UCL's Bioinformatics World Wide Web (WWW) server at http://www.biochem.ucl.ac.uk/bsm/dbbrowser / . We describe here progress with the database, its Web interface, and a recent exciting development: the integration of a novel colour alignment editor (http://www.biochem.ucl.ac.uk/bsm/dbbrowser++ +/CINEMA ), which allows visualisation and interactive manipulation of PRINTS alignments over the Internet.

MeSH Terms
Amino Acid Sequence Animals Computer Communication Networks Consensus Sequence/genetics Databases, Factual Proteins/genetics Sequence Alignment/methods User-Computer Interface
Chemicals
Proteins
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Attwood T K
Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WCIE 6BT, UK. attwood@bsm.bioc.ucl.ac.uk
Beck M E
Bleasby A J
Degtyarenko K
Michie A D
Parry-Smith D J
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/25.1.212
Email
attwood@bsm.bioc.ucl.ac.uk
Published
1997-01-01
Pages
212-7
Language
English
Region
England
NLM ID
0411011
PMCID
PMC146411
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/25.1.212 PMC Full Text View journal details
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