title: SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
abstract: The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysis. Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes a computational intensive task. The SIMAP database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. As of September 2009, SIMAP covers 48 million proteins and more than 23 million non-redundant sequences. Novel features of SIMAP include the expansion of the sequence space by including databases such as ENSEMBL as well as the integration of metagenomes based on their consistent processing and annotation. Furthermore, protein function predictions by Blast2GO are pre-calculated for all sequences in SIMAP and the data access and query functions have been improved. SIMAP assists biologists to query the up-to-date sequence space systematically and facilitates large-scale downstream projects in computational biology. Access to SIMAP is freely provided through the web portal for individuals (http://mips.gsf.de/simap/) and for programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and Web-Service (http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).
authors.affiliation: Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany. t.rattei@wzw.tum.de
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.forename: Patrick
authors.initials: P
authors.lastname: Tischler
authors.forename: Stefan
authors.initials: S
authors.lastname: Götz
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Jehl
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hoser
authors.forename: Roland
authors.initials: R
authors.lastname: Arnold
authors.forename: Ana
authors.initials: A
authors.lastname: Conesa
authors.forename: Hans-Werner
authors.initials: HW
authors.lastname: Mewes
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D016366:Open Reading Frames; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins