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Nucleic Acids Research 2006 34(Database Issue):D252-D256; doi:10.1093/nar/gkj106
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Nucleic Acids Research, 2006, Vol. 34, Database issue D252-D256
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

SIMAP: the similarity matrix of proteins

Thomas Rattei1,*, Roland Arnold2, Patrick Tischler2, Dominik Lindner1, Volker Stümpflen2 and H. Werner Mewes1,2

1Department of Genome Oriented Bioinformatics, Technical University of Munich Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany 2Institute for Bioinformatics, GSF-National Research Center for Environment and Health Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany

*To whom correspondence should be addressed. Tel: +49 8161 712132; Fax: +49 8161 712186; Email: t.rattei{at}wzw.tum.de

Received August 15, 2005. Revised October 17, 2005. Accepted October 17, 2005.

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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