title: SIMAP: the similarity matrix of proteins.
abstract: 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.
authors.affiliation: Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany. t.rattei@wzw.tum.de
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.forename: Roland
authors.initials: R
authors.lastname: Arnold
authors.forename: Patrick
authors.initials: P
authors.lastname: Tischler
authors.forename: Dominik
authors.initials: D
authors.lastname: Lindner
authors.forename: Volker
authors.initials: V
authors.lastname: Stümpflen
authors.forename: H Werner
authors.initials: HW
authors.lastname: Mewes
mesh_terms: D030562:Databases, Protein; D020407:Internet; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software; D014584:User-Computer Interface