HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot.
复制标题
DOI：
10.1093/nar/gkn661
复制
发表时间：
2009-01
影响因子：
14.9
通讯作者：
Bairoch A
中科院分区：
文献类型：
--
作者：
Lima T;Auchincloss AH;Coudert E;Keller G;Michoud K;Rivoire C;Bulliard V;de Castro E;Lachaize C;Baratin D;Phan I;Bougueleret L;Bairoch A
完全测序的微生物基因组（细菌和古细菌）的数量的增长产生了对尽可能多的蛋白质序列提供UniprotkB/Swiss-Prot质量注释的过程。我们已经设计了一个半自动化系统，HAMAP（对微生物蛋白质组的高质量自动化和手动注释），该系统使用非常严格的标准使用手动构建注释模板，以向所有手动定义的蛋白质家族的成员传播注释。 HAMAP系统由两个数据库组成：蛋白质组数据库和家庭数据库以及自动注释管道。蛋白质组数据库包括每个完全测序的微生物蛋白质组的生物学和序列信息，并提供了几种用于CDS搜索，爆炸选项和检索特定蛋白质集的工具。该家族数据库目前包括1500多个手动策划的蛋白质家族及其注释模板，这些模板用于注释属于Hamap家族之一的蛋白质。在Hamap网站上，可以扫描所有序列以及整个基因组。该系统提供警告，警告缺乏保守的氨基酸残基，异常序列长度等。由于实施了HAMAP，在Uniprotkb/Swiss-Prot（HAMAP网站：http：// http：// http：// http：// http：// www.expasy.org/sprot/hamap）。
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: http://www.expasy.org/sprot/hamap).
登录
查看更多内容
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
基因组再保管：Wiki解决方案？
影响因子：
12.3
作者：
通讯作者：
--
影响因子：
7
作者：
Wolf, YI;Rogozin, IB;Koonin, EV
通讯作者：
Koonin, EV
影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC
影响因子：
3.1
作者：
Gattiker, A;Michoud, K;Bairoch, A
通讯作者：
Bairoch, A