SUPERFAMILY 1.75 including a domain-centric gene ontology method.
SUPERFAMILY 1.75 including a domain-centric gene ontology method.
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DOI：
10.1093/nar/gkq1130
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发表时间：
2011-01
影响因子：
14.9
通讯作者：
Gough J
中科院分区：
文献类型：
--
作者：
de Lima Morais DA;Fang H;Rackham OJ;Wilson D;Pethica R;Chothia C;Gough J
SUPERFAMILY资源在蛋白质结构分类（SCOP）超家族水平上为超过1400个完全测序的基因组、超过120个宏基因组和其他基因集合（如UniProt）提供蛋白质结构域分配。所有的模型和作业都可以在http://supfam.org上浏览和下载。一个新的基于SCOP 1.75的隐马尔可夫模型库已经创建，一个以前被忽略的SCOP类，盘绕线圈，现在包括在内。我们的评分组件现在使用HMMER 3，它的速度快了几个数量级，并产生了上级结果。一个基于云的管道已经实现，并在亚马逊网络服务弹性计算机云上公开提供。SUPERFAMILY生命树参考系统得到了改进，允许用户在生命树上突出显示选定的超家族、家族或域架构。SUPERFAMILY最重要的进步是，现在它包含了一个基于域的基因本体论（GO）在超家族和家族水平。开发了一种新的方法来确保高质量的GO注释。新的方法是通用的，并已被用于生产领域为基础的表型本体论，除了GO。
The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 metagenomes and other gene collections such as UniProt. All models and assignments are available to browse and download at http://supfam.org. A new hidden Markov model library based on SCOP 1.75 has been created and a previously ignored class of SCOP, coiled coils, is now included. Our scoring component now uses HMMER3, which is in orders of magnitude faster and produces superior results. A cloud-based pipeline was implemented and is publicly available at Amazon web services elastic computer cloud. The SUPERFAMILY reference tree of life has been improved allowing the user to highlight a chosen superfamily, family or domain architecture on the tree of life. The most significant advance in SUPERFAMILY is that now it contains a domain-based gene ontology (GO) at the superfamily and family levels. A new methodology was developed to ensure a high quality GO annotation. The new methodology is general purpose and has been used to produce domain-based phenotypic ontologies in addition to GO.
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影响因子：
2.9
作者：
Lopez, Daniel;Pazos, Florencio
通讯作者：
Pazos, Florencio
影响因子：
3.7
作者：
Pethica R;Barker G;Kovacs T;Gough J
通讯作者：
Gough J
影响因子：
48
作者：
Flusberg, Benjamin A.;Webster, Dale R.;Lee, Jessica H.;Travers, Kevin J.;Olivares, Eric C.;Clark, Tyson A.;Korlach, Jonas;Turner, Stephen W.
通讯作者：
Turner, Stephen W.
影响因子：
14.9
作者：
Gough, J;Chothia, C
通讯作者：
Chothia, C
影响因子：
14.9
作者：
Madera, M;Vogel, C;Gough, J
通讯作者：
Gough, J