NAME

       Infernal  -  sequence  analysis  using  profiles  of  RNA sequence and secondary structure
       consensus

SYNOPSIS

       cmalign
         Align sequences to a covariance model

       cmbuild
         Construct  covariance  model(s)  from  structurally  annotated  RNA  multiple   sequence
       alignment(s)

       cmcalibrate
         Fit exponential tails for covariance model E-value determination

       cmconvert
         Convert Infernal covariance model files

       cmemit
         Sample sequences from a covariance model

       cmfetch
         Retrieve covariance model(s) from a file

       cmpress
         Prepare a covariance model database for cmscan

       cmscan
         Search sequence(s) against a covariance model database

       cmsearch
         Search covariance model(s) against a sequence database

       cmstat
         summary statistics for a covariance model file

DESCRIPTION

       Infernal is a suite of several programs for structural RNA sequence alignment and database
       homology search.  It  uses  probabilistic  models  called  "covariance  models"  (CMs)  to
       represent the likely evolutionary homologs of a multiple alignment (or single sequence) of
       a structural RNA sequence family.

       Along   with   the   Rfam    database    of    RNA    families    and    associated    CMs
       (http://rfam.sanger.ac.uk),  Infernal can be used to annotate homologs of known structural
       RNA families in genomes.

       Infernal is closely related to the HMMER software suite for sequence family analysis using
       profile  HMMs (http://hmmer.org), but is designed specifically for structural RNA sequence
       families.  In addition to modeling the conserved sequence of a family as profile HMMs  do,
       CMs  model  the family's conserved, well-nested (non-pseudoknotted) secondary structure as
       well. Consequently,  CM  search  and  alignment  methods  are  relatively  computationally
       expensive.  Infernal uses profile HMMs as filters and for deriving constraints to make the
       CM methods more practical.

       Infernal is used in three main modes: to search a sequence database for new homologs of an
       RNA family (or annotate homologs in a genome); to search a CM database (like Rfam) to find
       what known family a query sequence  belongs  to;  and  to  automatically  construct  large
       multiple  alignments  (i.e.  with an effectively unlimited number of sequences) using a CM
       representative of a sequence family.

       Suppose you have a structurally annotated multiple sequence alignment of  a  RNA  sequence
       family  of  interest,  and you want to search a sequence database for additional homologs.
       The cmbuild program builds covariance model(s) from multiple alignment(s) and  cmcalibrate
       determines  important  parameters  for estimating the statistical significance of database
       hits to the model in subsequent searches.

       The cmsearch program searches CM(s) against a sequence database.

       Suppose you have sequence(s) that you want to analyze using a Infernal-based  CM  database
       like  Rfam  (http://rfam.sanger.ac.uk).   The  cmpress  program formats a covariance model
       (such as the file you would download from Rfam) into  a  Infernal  binary  database.   The
       cmscan program searches sequence(s) against that database.

       Suppose  you  want  to  align  lots  of  sequences.  You  can construct a manageably small
       structural alignment of a representative set of sequences, build a CM  with  cmbuild,  and
       use the cmalign program to align any number of sequences to that CM.

       Infernal  also includes some auxiliary tools for working with large CM databases.  cmfetch
       fetches one or more CMs from a database.  cmstat prints  summary  statistics  about  a  CM
       file.

       For compatibility with previous versions of Infernal, as well as with HMMER, the cmconvert
       program converts CM files to a few other formats.

       The cmemit program generates (simulates) "homologous" sequences by sampling from a CM.  It
       can also generate a "consensus" sequence.

       Each program has its own man page.

SEE ALSO

       This  is  a  summary  man  page for the entire Infernal package.  See individual man pages
       [cmbuild(1), for example] for usage, options, and  description  of  each  program  in  the
       package.

       For  complete  documentation, see the user guide that came with your Infernal distribution
       (Userguide.pdf); or see the Infernal web page ().

COPYRIGHT

       Copyright (C) 2013 Howard Hughes Medical Institute.
       Freely distributed under the GNU General Public License (GPLv3).

       For additional information on copyright and licensing, see the file  called  COPYRIGHT  in
       your Infernal source distribution, or see the Infernal web page ().

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org