SIMAP—The similarity matrix of proteins
,*
1Institute for Bioinformatics, GSF-National Research Center for Environment and Health Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
2Department of Genome Oriented Bioinformatics, Technical University of Munich Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
*To whom correspondence should be addressed.
Motivation: Sequence similarity searches are of great importance in bioinformatics. Exhaustive searches for homologous proteins in databases are computationally expensive and can be replaced by a database of pre-calculated homologies in many cases. Retrieving similarities from an incrementally updated database instead of repeatedly recalculating them should provide homologs much faster and frees computational resources for other purposes.
Results: We have implemented SIMAP—a database containing the similarity space formed by almost all amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and allows incremental updates. We have implemented a powerful backbone for similarity computation, which is based on FASTA heuristics. By providing WWW interfaces as well as web services, we make our data accessible to the worldwide community. We have also adapted procedures to detect putative orthologs as example applications.
Availability: The SIMAP portal page providing links to SIMAP services is publicly available: http://mips.gsf.de/services/analysis/simap/. The web services can be accessed under http://mips.gsf.de/proj/hobitws/services/RPCSimapService?wsdl and http://mips.gsf.de/proj/hobitws/services/DocSimapService?wsdl
Contact: t.rattei{at}wzw.tum.de
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