SIMAP:: the similarity matrix of proteins

被引：38

作者：

Rattei, Thomas

Arnold, Roland

Tischler, Patrick

Lindner, Dominik

Stumpflen, Volker

Mewes, H. Werner

机构：

[1] Tech Univ Munich, Dept Genome Oriented Bioinformat, D-85350 Freising Weihenstephan, Germany

[2] GSF, Natl Res Ctr Environm & Hlth, Inst Bioinformat, D-85764 Neuherberg, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷

关键词：

D O I：

10.1093/nar/gkj106

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Similarity Matrix of Proteins (SIMAP) (http://mips.gsf.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 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.

引用

页码：D252 / D256

页数：5

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