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 0.81 [1 May 2007].

Documentation:

User's Guide [PDF, 59 pages] .
00README from the current release.

Download:

The current source code distribution: infernal 0.81 [tarball, 6.5 MB]
Infernal is freely available under the GPL .

There is a typo that will prevent 0.81 from compiling on a Mac OS/X system (only, as far as we know). To fix this, before you ./configure, go to easel/esl_config.h.in and add

   #undef HAVE_SYS_TYPES_H

somewhere (we have it in the "Systems headers" section of that file). This was supposed to be fixed in 0.81, but it still slipped through. We'll release a new version (really fixed this time) later this week.

Archived releases:

For reproducibility of published results, we have archived several older versions:

Release	Date	Download	Notes
0.1	April 2002	[infernal-0.1.tar.gz, 402 KB]	Version used in the divide and conquer algorithm paper (Eddy, 2002)
0.3	July 2002	[infernal-0.3.tar.gz, 431 KB]	Version used for the first Rfam release (Griffiths-Jones et al, 2003)
0.4	August 2002	[infernal-0.4.tar.gz, 443 KB]	cmalign first appears, and was used for final work on Rfam 1.0.
0.55	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)
0.6	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.
0.7	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.
0.71	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, manuscript submitted)
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, PLoS Computational Biology, in press)

Further reference:

Covariance models were originally described in (Eddy and Durbin, 1994). They were first implemented in the COVE software package.
The tRNA identification program tRNAscan-SE is based on a tRNA CM and COVE (Lowe and Eddy, 1997).
A chapter of Biological Sequence Analysis (Durbin et al., 1998) describes CMs in more detail.
The memory-efficient divide-and-conquer CYK alignment algorithm is described in (Eddy, 2002). A new implementation, Infernal, replaced COVE.
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 includes MPI parallelization and E-value calculations, features that Infernal still lacks.
The Rfam database of RNA families is based on the Infernal software (Griffiths-Jones, 2003; Griffiths-Jones, 2005) .
The QDB query-dependent banded dynamic programming algorithm used to increase search speed is described in (Nawrocki and Eddy, submitted), along with mixture Dirichlet priors and entropy weighting.

Road map

The 0.81 release now includes all but a few smallish features that we consider to be necessary before declaring a 1.0 release, including E-values, MPI parallelization, and integration of Robbie Klein's RSEARCH program (which forked off of Infernal a few years ago). We anticipate a 1.0 release after some final cleanup.

We welcome code contributions, feature requests, and bug reports.

Sean Eddy

Last modified: Tue May 1 13:17:51 2007