SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.
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DOI：
10.1093/nar/gkn762
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发表时间：
2009-01
影响因子：
14.9
通讯作者：
Gough J
中科院分区：
文献类型：
--
作者：
Wilson D;Pethica R;Zhou Y;Talbot C;Vogel C;Madera M;Chothia C;Gough J
超家族为来自所有完全测序基因组的蛋白质以及大序列集合（例如Uniprot）提供结构，功能和进化信息。数据库中包括900多个基因组的蛋白质域分配，可以在http://supfam.org/上访问。基于蛋白质结构分类（SCOP）域定义的隐藏Markov模型用于提供结构注释。我们最近根据SCOP 1.73制作了一个新的模型库。家庭级分配也可用。从网站中，用户可以提交scop域分类的序列；搜索关键字，例如超家族，家庭，有机体名称，模型和序列标识符；相对于其他基因组或基因组组，在基因组中找到过多的和不足的家族或超家族。比较跨基因组选择的域体系结构，并最终在蛋白质数据库（PDB），基因组和自定义序列之间构建多个序列比对。该数据库的最新扩展包括超级家庭的摘要和基因本体术语，对生命之树的家庭分布的分类可视化，寻找功能相似的领域体系结构和系统发育树。数据库，模型和相关脚本可从FTP网站下载。
SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidden Markov models based on Structural Classification of Proteins (SCOP) domain definitions at the superfamily level are used to provide structural annotation. We recently produced a new model library based on SCOP 1.73. Family level assignments are also available. From the web site users can submit sequences for SCOP domain classification; search for keywords such as superfamilies, families, organism names, models and sequence identifiers; find over- and underrepresented families or superfamilies within a genome relative to other genomes or groups of genomes; compare domain architectures across selections of genomes and finally build multiple sequence alignments between Protein Data Bank (PDB), genomic and custom sequences. Recent extensions to the database include InterPro abstracts and Gene Ontology terms for superfamiles, taxonomic visualization of the distribution of families across the tree of life, searches for functionally similar domain architectures and phylogenetic trees. The database, models and associated scripts are available for download from the ftp site.
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Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
拟南芥信息资源（TAIR）：基因结构和功能注释。
影响因子：
14.9
作者：
Swarbreck, David;Wilks, Christopher;Lamesch, Philippe;Berardini, Tanya Z.;Garcia-Hernandez, Margarita;Foerster, Hartmut;Li, Donghui;Meyer, Tom;Muller, Robert;Ploetz, Larry;Radenbaugh, Amie;Singh, Shanker;Swing, Vanessa;Tissier, Christophe;Zhang, Peifen;Huala, Eva
通讯作者：
Huala, Eva
影响因子：
14.9
作者：
Mulder NJ;Apweiler R;Attwood TK;Bairoch A;Bateman A;Binns D;Bork P;Buillard V;Cerutti L;Copley R;Courcelle E;Das U;Daugherty L;Dibley M;Finn R;Fleischmann W;Gough J;Haft D;Hulo N;Hunter S;Kahn D;Kanapin A;Kejariwal A;Labarga A;Langendijk-Genevaux PS;Lonsdale D;Lopez R;Letunic I;Madera M;Maslen J;McAnulla C;McDowall J;Mistry J;Mitchell A;Nikolskaya AN;Orchard S;Orengo C;Petryszak R;Selengut JD;Sigrist CJ;Thomas PD;Valentin F;Wilson D;Wu CH;Yeats C
通讯作者：
Yeats C
影响因子：
3.4
作者：
Rasteiro, Rita;Pereira-Leal, Jose B.
通讯作者：
Pereira-Leal, Jose B.
影响因子：
14.9
作者：
Bru C;Courcelle E;Carrère S;Beausse Y;Dalmar S;Kahn D
通讯作者：
Kahn D