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Infernal - inference of RNA secondary structure alignments
http://infernal.janelia.org/
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:: About this software:
Infernal is an implementation of "covariance models" (CMs), which
are statistical models of RNA secondary structure and sequence
consensus.
You give Infernal a multiple sequence alignment of a conserved
structural RNA family, annotated with the consensus secondary
structure. The "cmbuild" program builds a statistical profile of
your alignment. That CM can be used as a query in a database
search to find more homologs of your RNAs (the "cmsearch"
program). You can also use a CM of a representative alignment of
your sequence family to create a larger consensus alignment of
any number of RNAs.
We still consider this software to be under development. Our
research efforts are focused on reducing the computatational
complexity of CM algorithms so searches are faster. We haven't
yet spent as much effort as we'd like on making Infernal pretty
and user-friendly. Nonetheless, Infernal provides the software
engines behind the Rfam RNA database (http://rfam.janelia.org).
:: Getting Infernal:
WWW: http://infernal.janelia.org/
Distro tarballs: ftp://selab.janelia.org/pub/software/infernal/
:: Developer access (password required):
SVN: https://svn.janelia.org/eddylab/eddys/src/infernal
:: Installation:
See the Userguide.pdf for complete instructions. In brief:
% ./configure
% make
The programs will be in the src/ subdirectory.
Additionally, 'make check' will run an automated test suite, and
'make install' will install the programs in /usr/local/bin by
default.
:: Getting started:
For documentation, including installation instructions and a
tutorial, see the Infernal User's Guide: Userguide.pdf.
:: Reference:
- EP Nawrocki, DL Kolbe, and SR Eddy, "Infernal 1.0: inference of
RNA alignments" Bioinformatics 25:1335-1337 (2009).
:: Other references:
- DL Kolbe and SR Eddy, "Local RNA structure alignment with
incomplete sequence", Bioinformatics 25:1236-1243 (2009).
- EP Nawrocki and SR Eddy, "Query-dependent banding (QDB) for
faster RNA similarity searches", PLoS Computational Biology,
3:e56 (2007).
- SR Eddy, "A memory efficient dynamic programming algorithm for
optimal structural alignment of a sequence to an RNA secondary
structure", BMC Bioinformatics, 3:18 (2002).
- R Durbin, S Eddy, A Krogh, G Mitchison. Biological Sequence
Analysis: Probabilistic Models of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge UK. (1998).
- S.R. Eddy and R. Durbin, "RNA sequence analysis using
covariance models", Nucl. Acids Res. 22:2079-2088 (1994).
:: Credits:
The current Infernal developer team at HHMI Janelia Farm:
Diana Kolbe, Eric Nawrocki, and Sean Eddy.
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