SIMAP: the similarity matrix of proteins

Research output: Contribution to journalArticlepeer-review


  • Thomas Rattei
  • Patrick Tischler
  • Dominik Lindner
  • Volker Stümpflen
  • H Werner Mewes

Colleges, School and Institutes

External organisations

  • Technical University Munich


Similarity Matrix of Proteins (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.


Original languageEnglish
Pages (from-to)D252-6
JournalNucleic Acids Research
Issue numberDatabase issue
Publication statusPublished - 1 Jan 2006


  • Databases, Protein, Internet, Sequence Alignment, Sequence Homology, Amino Acid, Software, User-Computer Interface, Journal Article, Research Support, Non-U.S. Gov't