HMMER web server: interactive sequence similarity searching.
HMMER web server: interactive sequence similarity searching.
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DOI：
10.1093/nar/gkr367
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发表时间：
2011-07
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;Eddy SR
HMMER是使用概率方法进行蛋白质序列相似性搜索的软件套件。以前，HMMER主要只作为计算密集型UNIX命令行工具提供，限制了其使用。软件HMMER 3的最新进展使速度比以前的版本提高了100倍。现在，通过网络进行高效的轮廓隐马尔可夫模型（轮廓HMM）搜索是可行的。HMMER网络服务器（hmmer.janelia.org）已经被设计和实现，使得大多数蛋白质数据库搜索在几秒钟内返回。方法可用于针对靶序列数据库搜索单个蛋白质序列、多个蛋白质序列比对或谱HMM，以及针对Pfam搜索蛋白质序列。Web服务器的设计是为了满足一系列不同的用户专业知识，并接受一次批量上传多个查询。所有的搜索方法也都可以作为RESTful Web服务使用，从而使它们可以很容易地集成为本地脚本工作流中的远程执行任务。我们专注于最大限度地减少搜索时间和快速显示表格结果的能力，无论找到的匹配数量如何，开发搜索结果的图形摘要以提供快速，直观的评估。
HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.
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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
影响因子：
14.9
作者：
Lees J;Yeats C;Redfern O;Clegg A;Orengo C
通讯作者：
Orengo C
影响因子：
14.9
作者：
de Lima Morais DA;Fang H;Rackham OJ;Wilson D;Pethica R;Chothia C;Gough J
通讯作者：
Gough J
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
14.9
作者：
Bhagat J;Tanoh F;Nzuobontane E;Laurent T;Orlowski J;Roos M;Wolstencroft K;Aleksejevs S;Stevens R;Pettifer S;Lopez R;Goble CA
通讯作者：
Goble CA