Infernal 1.1: 100-fold faster RNA homology searches.
Infernal 1.1: 100-fold faster RNA homology searches.
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地狱1.1：RNA同源性搜索速度更快100倍。
DOI：
10.1093/bioinformatics/btt509
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发表时间：
2013-11-15
期刊：
影响因子：
--
通讯作者：
Eddy SR
中科院分区：
文献类型：
--
作者：
Nawrocki EP;Eddy SR
摘要：地狱构建了从结构注释的多个序列对准的RNA家族的序列和二级结构，称为输入。隐藏的Markov模型（HMM）方法和HMM带的CM比对方法。这使得在先前版本上可以加速约100倍，而在详尽的非过滤CM搜索上可以实现约10 000倍的加速度。
可用性：源代码，文档和基准可从http://infernal.janelia.org下载。
联系人：nawrockie@janelia.hhmi.org
Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches. Availability: Source code, documentation and the benchmark are downloadable from http://infernal.janelia.org. Infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Documentation includes a user’s guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software. Contact: nawrockie@janelia.hhmi.org
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影响因子：
14.9
作者：
Griffiths-Jones, S;Bateman, A;Eddy, SR
通讯作者：
Eddy, SR
影响因子：
5.8
作者：
Weinberg, Zasha;Ruzzo, Walter L.
通讯作者：
Ruzzo, Walter L.
影响因子：
5.8
作者：
Weinberg, Z;Ruzzo, WL
通讯作者：
Ruzzo, WL
影响因子：
14.9
作者：
Cole JR;Wang Q;Cardenas E;Fish J;Chai B;Farris RJ;Kulam-Syed-Mohideen AS;McGarrell DM;Marsh T;Garrity GM;Tiedje JM
通讯作者：
Tiedje JM
影响因子：
7
作者：
Freyhult, Eva K.;Bollback, Jonathan P.;Gardner, Paul P.
通讯作者：
Gardner, Paul P.