SIMAP--the similarity matrix of proteins

Roland Arnold, Thomas Rattei, Patrick Tischler, Minh-Duc Truong, Volker Stümpflen, Werner Mewes

Research output: Contribution to journalArticlepeer-review

31 Citations (Scopus)

Abstract

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

Original languageEnglish
Pages (from-to)ii42-ii46
JournalBioinformatics
Volume21
Issue numberSupplement 2
DOIs
Publication statusPublished - 1 Sep 2005

Keywords

  • Algorithms
  • Amino Acid Sequence
  • Computer Simulation
  • Database Management Systems
  • Databases, Protein
  • Information Storage and Retrieval
  • Models, Chemical
  • Models, Molecular
  • Molecular Sequence Data
  • Proteins
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Sequence Homology, Amino Acid
  • Software
  • User-Computer Interface
  • Journal Article

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