Infernal: inference of RNA alignments

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 1.1rc2 [14 Dec 2012].

Documentation:

User's Guide [PDF, 125 pages] .
README from the current release.
Release notes for the current release.

Reference:

The recommended citation for using Infernal is E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy, Infernal 1.0: Inference of RNA alignments , Bioinformatics 25:1335-1337 (2009), .

Download:

The current source code distribution: infernal 1.1rc2, source only [tarball, 18.2 MB]
Source with binaries: infernal 1.1rc2 with Linux/Intel binaries [tarball, 30.2 MB] , infernal 1.1rc2 with MacOSX/Intel binaries [tarball, 30.1 MB]
Infernal is freely available under the GNU General Public License version 3 [GPLv3].
We welcome code contributions, feature requests, and bug reports.

Note on the Rfam transition to Infernal 1.1

The current Rfam 11.0 database is built on Infernal 1.0. This means that CM files from Rfam cannot be used directly with Infernal 1.1. If you'd like to use Infernal 1.1 for Rfam 11.0 work, you have three options.

First, you can use the cmconvert program in Infernal 1.1 to convert the 1.0 files from Rfam. Second, you can download all converted Rfam 11.0 CMs in a single gzipped CM file in 1.1 format, and use that. With these first two options, the models will be parameterized identically to the 1.0 built Rfam 11.0 models available from the Rfam website, so identical hits using the 1.0 and 1.1 files will have identical bit scores. You'll want to use one of these two options if you want to reproduce scores obtained with the Infernal 1.0 Rfam files.

The third option is to download a file with newly built and parameterized Rfam 11.0 CMs created by Infernal 1.1's cmbuild and cmcalibrate . These models were built from the Rfam 11.0 seed alignments but using Infernal 1.1's parameterization methods. With this third option, the models will have slightly different parameters than the Infernal 1.0 Rfam 11.0 CM files, so the same hit will likely get a different score and E-value using these models compared with using the Infernal 1.0 Rfam 11.0 models. However, our benchmarking suggests that the new parameterization makes the models slightly more sensitive, so you may want to choose this option if you're not worried about reproducing Rfam 11.0 bit scores.

Alternatively, you can continue using the previous Infernal 1.0.2 release for Rfam work until Rfam makes the transition to Infernal 1.1.

Further reference:

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 Rfam database of RNA families is based on the Infernal software (Griffiths-Jones, 2003; Griffiths-Jones, 2005) .
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. Other releases are also archived on our FTP site, but these are the main mileposts:

Release	Date	Download	Notes
1.0.2	Oct 2009	[infernal-1.0.2.tar.gz, 15.2 MB]	Last release before the major 1.1 update. This was the "current" version for nearly three years.
1.0.1	Oct 2009	[infernal-1.0.1.tar.gz, 15.2 MB]	Version that reproduces the results in Eric Nawrocki's thesis, (Nawrocki, 2009)
1.0	Jan 2009	[infernal-1.0.tar.gz, 15.0 MB]	Version described in the first "official" release paper, (Nawrocki et al., 2009)
0.81	May 2007	[infernal-0.81.tar.gz, 6.5 MB]	First version with E-values and MPI parallelization.
0.72	January 2007	[infernal-0.72.tar.gz, 6.0 MB]	Version used for the published version of the QDB algorithm paper (Nawrocki and Eddy, 2007)
0.71	November 2006	[infernal-0.71.tar.gz, 6.0 MB]	Version used in the submitted version of the QDB algorithm manuscript (Nawrocki and Eddy, 2007)
0.7	December 2005	[infernal-0.7.tar.gz, 4.3 MB]	Entropy weighting incorporated. This version was used by Paul Gardner and Eva Freyhult in their BRaliBaseIII benchmark.
0.6	November 2005	[infernal-0.6.tar.gz, 4.3 MB]	Mixture Dirichlets incorporated, under pressure from Paul Gardner and Eva Freyhult's ongoing benchmarking work.
0.55	April 2003	[infernal-0.55.tar.gz, 763 KB]	First version with documentation. Rfam 2.0 through Rfam 7.0 are based on 0.5x code (Griffiths-Jones et al, 2005)
0.4	August 2002	[infernal-0.4.tar.gz, 443 KB]	cmalign first appears, and was used for final work on Rfam 1.0.
0.3	July 2002	[infernal-0.3.tar.gz, 431 KB]	Version used for the first Rfam release (Griffiths-Jones et al, 2003)
0.1	April 2002	[infernal-0.1.tar.gz, 402 KB]	Version used in the divide and conquer algorithm paper (Eddy, 2002)

Sean Eddy

Last modified: Mon Dec 17 05:17:35 2012