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SIMAP: The similarity matrix of proteins.
Nucleic Acids Res. 34, 252-256 (2006)
Similarity Matrix of Proteins (SIMAP) (http://mips.gsf.de/simap) provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith-Waterman algorithm. Our ProtInfo system allows querying by protein sequences covered by the SIMAP dataset as well as by fragments of these sequences, highly similar sequences and title words. Each sequence in the database is supplemented with pre-calculated features generated by detailed sequence analyses. By providing WWW interfaces as well as web-services, we offer the SIMAP resource as an efficient and comprehensive tool for sequence similarity searches.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
GENOME DATABASE; SMITH-WATERMAN; SEQUENCE; IDENTIFICATION; CLUSTR; SPACE
ISSN (print) / ISBN
0305-1048
e-ISSN
1362-4962
Journal
Nucleic Acids Research
Quellenangaben
Volume: 34,
Issue: SI,
Pages: 252-256
Publisher
Oxford University Press
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Reviewing status
Peer reviewed