SIMAP: the similarity matrix of proteins

Abstract

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.

Figure 1

Illustration of the list of homologs for the UNIPROT protein Q06124, the human protein-tyrosine phosphatase, non-receptor type 11. Starting from the fulltext search using ProtInfo, the list of homologs can be accessed. From a list of homologs, for every hit links to the pairwise alignment, the report page and the list of its homologs are provided. Additionally the filter options and search scope for the list of homologs can be modified.