SIMAP—The similarity matrix of proteins

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 updat...

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Bibliographic Details
Published in:Bioinformatics 2005-09, Vol.21 (suppl-2), p.ii42-ii46
Main Authors: Arnold, Roland, Rattei, Thomas, Tischler, Patrick, Truong, Minh-Duc, Stümpflen, Volker, Mewes, Werner
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Sequence
Computer Simulation
Database Management Systems
Databases, Protein
Information Storage and Retrieval - methods
Models, Chemical
Models, Molecular
Molecular Sequence Data
Proteins - chemistry
Proteins - ultrastructure
Sequence Alignment - methods
Sequence Analysis, Protein - methods
Sequence Homology, Amino Acid
Software
User-Computer Interface
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Summary: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@wzw.tum.de
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bti1107