Infernal: inference of RNA alignments infernal home | rfam database | eddy lab |

Overview:

Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

The latest release of Infernal is 1.1.5 [7 Sep 2023].

Documentation:

• User's Guide [PDF, 119 pages] .
• README from the current release.
• Release notes for the current release.

Reference:

• The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics 29:2933-2935 (2013).

Downloads:

• The current source code: [Infernal 1.1.5 source tarball, 31.3 MB]
• Source with binaries:
  [infernal 1.1.5 with Linux/Intel binaries, 48.4 MB]
  [infernal 1.1.5 with MacOSX/Silicon binaries, 45.5 MB]
  [infernal 1.1.5 with MacOSX/Intel binaries, 46.7 MB]

Or, install using a package manager:

• Debian package, thanks to Michael Crusoe. If you are using Debian, you can install with:
  sudo apt-get install infernal infernal-doc
• Bioconda package, thanks to Björn Grüning. If you have conda, you can install with:
  conda install -c bioconda infernal
• Homebrew Science package. With homebrew, you can install with
  brew tap brewsci/bio
brew install infernal

Other useful Infernal resources:

• The Infernal GitHub repository.
• BioContainer wrapper, thanks to Björn Grüning.
• Galaxy wrapper, also thanks to Björn Grüning.

Contact us:

• We welcome bug reports, feature requests, and code contributions. Email us at: sean@eddylab.org.
  

Internal benchmark:

• The Infernal 1.1 Bioinformatics publication contains results from our internal RMARK3 benchmark. Files necessary for reproducing that benchmark are available here.

Further reference:

• The Rfam database of RNA families is based on the Infernal software. This article demonstrates how to use the Rfam database and website and includes a section on using Infernal for genome annotation. Rfam 14 is described in (Kalvari, 2020).
• This paper details the discovery of group I introns in archaea using Infernal.
• This book chapter explains how to use Infernal and Rfam to annotate RNAs in genomes.
• Infernal-based identification of functional RNAs in metagenomic datasets is discussed in (Nawrocki and Eddy, 2013).
• Version 1.0 of Infernal was announced in a 2009 Bioinformatics applications note.
• Several improvements in Infernal 1.0, including techniques used to improve speed performance, are described in Eric Nawrocki's 2009 Ph.D. thesis.
• The trCYK local alignment algorithm is described in (Kolbe and Eddy, 2009).
• The QDB query-dependent banded dynamic programming algorithm used to increase search speed is described in (Nawrocki and Eddy, 2007), along with mixture Dirichlet priors and entropy weighting.
• The RSEARCH software for searching with single RNA structures (instead of with profiles built from multiple alignments) is based on Infernal's alignment engines (Klein and Eddy, 2003). RSEARCH also included MPI parallelization and E-value calculations, features that were merged back into Infernal in Infernal 1.0.
• The memory-efficient divide-and-conquer CYK alignment algorithm is described in (Eddy, 2002). A new implementation, Infernal, replaced COVE.
• A chapter of Biological Sequence Analysis (Durbin et al., 1998) describes CMs in more detail.
• The tRNA identification program tRNAscan-SE is based on a tRNA CM and COVE (Lowe and Eddy, 1997).
• Covariance models were originally described in (Eddy and Durbin, 1994). They were first implemented in the COVE software package.

Archived releases:

For reproducing published results, the following archived older versions may be of interest: