SIMAP - The similarity matrix of proteins

Similarity Matrix of Proteins (SIMAP) (http://mips.gsf. 10 de/simap) provides a database based on a precomputed 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 15 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 20 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 25 sequence analyses. By providing WWW interfaces as well as web-services, we offer the SIMAP resource as anefficientandcomprehensivetoolforsequencesimilarity searches.

• Type: Conference
• Year: 2005
• Where: ECCB
• Authors: Roland Arnold, Thomas Rattei, Patrick Tischler, Minh-Duc Truong, Volker Stümpflen, Hans-Werner Mewes
• Keywords: ECCB 2005, Precomputed Similarity Matrix, Sequence Similarity Searches, Similarity Matrix