PairsDB atlas of protein sequence space

被引：11

作者：

Heger, Andreas ^{[1
,2
]}

Korpelainen, Eija ^{[3
]}

Hupponen, Taavi ^{[3
]}

Mattila, Kimmo ^{[3
]}

Ollikainen, Vesa ^{[3
]}

Holm, Liisa ^{[1
,4
]}

机构：

[1] Univ Helsinki, Inst Biotechnol, FIN-00014 Helsinki, Finland

[2] Univ Oxford, MRC, Funct Genet Unit, Oxford OX1 2JD, England

[3] CSC, Espoo, Finland

[4] Univ Helsinki, Dept Biol & Environm Sci, Div Genet, FIN-00014 Helsinki, Finland

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

基金：

英国医学研究理事会;

关键词：

D O I：

10.1093/nar/gkm879

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 [生物化学与分子生物学]; 081704 [应用化学];

摘要：

Sequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy. Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually on each request, results are retrieved instantaneously from a database of pre-computed alignments. Filtering options allow you to find a set of sequences satisfying a set of criteria - for example, all human proteins with solved structure and without transmembrane segments. PairsDB is continually updated and covers all sequences in Uniprot. The data is stored in a MySQL relational database. Data files will be made available for download at ftp://nic.funet.fi/pub/sci/molbio. PairsDB can also be accessed interactively at http://pairsdb.csc.fi. PairsDB data is a valuable platform to build various downstream automated analysis pipelines. For example, the graph of all-against-all similarity relationships is the starting point for clustering protein families, delineating domains, improving alignment accuracy by consistency measures, and defining orthologous genes. Moreover, query-anchored stacked sequence alignments, profiles and consensus sequences are useful in studies of sequence conservation patterns for clues about possible functional sites.

引用

页码：D276 / D280

页数：5

共 25 条

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