Infernal 1.1: 100-fold faster RNA homology searches

被引：2353

作者：

Nawrocki, Eric P. ^{[1
]}

Eddy, Sean R. ^{[1
]}

机构：

[1] HHMI Janelia Farm Res Campus, Ashburn, VA 20147 USA

来源：

BIOINFORMATICS | 2013年 / 29卷 / 22期

关键词：

NONCODING RNA; DATABASE; ALIGNMENTS; ANNOTATION; SEQUENCE; FAMILIES; RFAM;

D O I：

10.1093/bioinformatics/btt509

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 similar to 100-fold acceleration over the previous version and similar to 10 000-fold acceleration over exhaustive non-filtered CM searches.

引用

页码：2933 / 2935

页数：3

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