HMMER web server: 2015 update.
HMMER web server: 2015 update.
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DOI：
10.1093/nar/gkv397
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发表时间：
2015-07-01
影响因子：
14.9
通讯作者：
Eddy SR
中科院分区：
文献类型：
--
作者：
Finn RD;Clements J;Arndt W;Miller BL;Wheeler TJ;Schreiber F;Bateman A;Eddy SR
HMMER网站，可在http：//www.ebi.ac.uk/Tools/hmmer/获得，提供对HMMER软件套件中发现的蛋白质同源性搜索算法的访问。自2011年网站首次发布以来，搜索功能已经扩展到包括迭代搜索算法jackhmmer。靶序列数据库的持续增长意味着显著序列命中的传统表格表示可能对用户来说是压倒性的。因此，已经开发了呈现同源性搜索结果的其他方式，允许根据分类学分布或结构域架构对其进行总结。分类法和域体系结构表示可以组合使用，以根据用户的需要过滤结果。还可以在提交之前使用新的分类过滤器来限制搜索，这不仅确保了结果特定于所请求的分类组，而且还提高了搜索性能。用于蛋白质家族和结构域的查询序列注释的轮廓隐马尔可夫模型库的库已经扩展到包括来自CATH-Gene 3D、PIRSF、Superfamily和TIGRFAM的库。最后，我们讨论了搬迁的HMMER网络服务器的欧洲生物信息学研究所和潜在的影响，这将有。
The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
14.9
作者：
Haft DH;Selengut JD;Richter RA;Harkins D;Basu MK;Beck E
通讯作者：
Beck E
影响因子：
5.6
作者：
KROGH, A;BROWN, M;HAUSSLER, D
通讯作者：
HAUSSLER, D
影响因子：
14.9
作者：
Gutmanas A;Alhroub Y;Battle GM;Berrisford JM;Bochet E;Conroy MJ;Dana JM;Fernandez Montecelo MA;van Ginkel G;Gore SP;Haslam P;Hatherley R;Hendrickx PM;Hirshberg M;Lagerstedt I;Mir S;Mukhopadhyay A;Oldfield TJ;Patwardhan A;Rinaldi L;Sahni G;Sanz-García E;Sen S;Slowley RA;Velankar S;Wainwright ME;Kleywegt GJ
通讯作者：
Kleywegt GJ
影响因子：
14.9
作者：
Wu, CH;Nikolskaya, A;Barker, WC
通讯作者：
Barker, WC