HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

被引：120

作者：

Lima, Tania ^{[1
]}

Auchincloss, Andrea H. ^{[1
]}

Coudert, Elisabeth ^{[1
]}

Keller, Guillaume ^{[1
]}

Michoud, Karine ^{[1
]}

Rivoire, Catherine ^{[1
]}

Bulliard, Virginie ^{[1
]}

de Castro, Edouard ^{[1
]}

Lachaize, Corinne ^{[1
]}

Baratin, Delphine ^{[1
]}

Phan, Isabelle ^{[1
]}

Bougueleret, Lydie ^{[1
]}

Bairoch, Amos ^{[1
]}

机构：

[1] Swiss Inst Bioinformat, Swiss Prot Grp, CH-1211 Geneva 4, Switzerland

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

基金：

美国国家卫生研究院;

关键词：

GENOME; ANNOTATION; ALIGNMENT;

D O I：

10.1093/nar/gkn661

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：

The growth in the number of completely sequenced microbial genomes (bacterial and archaeal) has generated a need for a procedure that provides UniProtKB/Swiss-Prot-quality annotation to as many protein sequences as possible. We have devised a semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. The HAMAP system is composed of two databases, the proteome database and the family database, and of an automatic annotation pipeline. The proteome database comprises biological and sequence information for each completely sequenced microbial proteome, and it offers several tools for CDS searches, BLAST options and retrieval of specific sets of proteins. The family database currently comprises more than 1500 manually curated protein families and their annotation templates that are used to annotate proteins that belong to one of the HAMAP families. On the HAMAP website, individual sequences as well as whole genomes can be scanned against all HAMAP families. The system provides warnings for the absence of conserved amino acid residues, unusual sequence length, etc. Thanks to the implementation of HAMAP, more than 200 000 microbial proteins have been fully annotated in UniProtKB/Swiss-Prot (HAMAP website: www.expasy.org/sprot/hamap).

引用

页码：D471 / D478

页数：8

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