Infernal: inference of RNA alignments
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].
We welcome code contributions, feature requests, and bug reports.
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.
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:
|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|