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) 2019 Howard Hughes Medical Institute.
       Freely distributed under the BSD open source license.

       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