SIMAP
NAR Molecular Biology Database Collection entry number 867
Technical University of Munich and GSF-National Research Center for Environment and Health, Neuherberg, Germany
Contact t.rattei@wzw.tum.de
Database Description
SIMAP provides a database based on a pre-computed similarity matrix covering the similarity space formed by more than 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 using protein sequences covered by the SIMAP data set as well as 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.
Category: Protein sequence databases
Subcategory: Protein domain databases; protein classification
Go to the abstract in the NAR 2008 Database Issue.
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