Infernal 1.1: 100-fold faster RNA homology searches

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

• Publication year

  2013

• Venue

  Bioinform.

• Publication date

  2013-09-04

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btt509PMID 24008419PMCID 3810854
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Rfam 11.0: 10 years of RNA families

  2012cited by this paper
• Accelerated Profile HMM Searches

  2011influential reference
• Structural rna homology search and alignment using covariance models

  2009influential reference
• Infernal 1.0: inference of RNA alignments

  2009cited by this paper
• Local RNA structure alignment with incomplete sequence

  2009influential reference
• A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

  2008influential reference
• The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

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• Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA.

  2006cited by this paper
• Sequence-based heuristics for faster annotation of non-coding RNA families

  2006cited by this paper
• Supplement to : Exploiting Conserved Structure for Faster Annotation of Non-coding RNAs Without Loss of Accuracy

  2004cited by this paper
• Rfam: an RNA family database

  2003cited by this paper
• Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars

  2000influential reference
• Homology Detection via Family Pairwise Search

  1998influential reference
• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

  1998cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Defining 3D residue environment in protein structures using SCORPION and FORMIGA

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