SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
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DOI：
10.1093/nar/30.1.268
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发表时间：
2002-01-01
影响因子：
14.9
通讯作者：
Chothia, C
中科院分区：
文献类型：
--
作者：
Gough, J;Chothia, C
SUPERFAMILY数据库包含一个隐马尔可夫模型库，代表所有已知结构的蛋白质。该数据库基于SCOP“超家族”水平的蛋白质结构域分类，该分类将具有共同进化祖先的最远相关蛋白质组合在一起。在http://supfam.org上有一个公共服务器，它提供三种服务：序列搜索，已知结构序列的多重比对，以及所有完整基因组的结构分配。给定氨基酸或核苷酸查询序列，服务器将返回域架构和SCOP分类。服务器产生查询序列与已知结构的序列的比对，并且包括基因组和PDB序列的多个比对。对所有完整的基因组（目前为59个）进行结构分配，覆盖约一半的可溶性蛋白质结构域。分配，超家庭细分和统计数据，他们可以从服务器。该数据库目前被该小组和其他人用于基因组注释、结构基因组学、基因预测和基于域的基因组研究。
The SUPERFAMILY database contains a library of hidden Markov models representing all proteins of known structure. The database is based on the SCOP 'superfamily' level of protein domain classification which groups together the most distantly related proteins which have a common evolutionary ancestor. There is a public server at http://supfam.org which provides three services: sequence searching, multiple alignments to sequences of known structure, and structural assignments to all complete genomes. Given an amino acid or nucleotide query sequence the server will return the domain architecture and SCOP classification. The server produces alignments of the query sequences with sequences of known structure, and includes multiple alignments of genome and PDB sequences. The structural assignments are carried out on all complete genomes (currently 59) covering approximately half of the soluble protein domains. The assignments, superfamily breakdown and statistics on them are available from the server. The database is currently used by this group and others for genome annotation, structural genomics, gene prediction and domain-based genomic studies.