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NAME

       hmmalign - align sequences to an HMM profile

SYNOPSIS

       hmmalign [options] hmmfile seqfile

DESCRIPTION

       hmmalign  reads  an  HMM  file from hmmfile and a set of sequences from
       seqfile, aligns the  sequences  to  the  profile  HMM,  and  outputs  a
       multiple sequence alignment.

       seqfile  may  be  in  any  unaligned or aligned file format accepted by
       HMMER. If it is in a multiple alignment format  (e.g.  Stockholm,  MSF,
       SELEX,   ClustalW),  the  existing  alignment  is  ignored  (i.e.,  the
       sequences are read as if they were unaligned - hmmalign will align them
       the way it wants).

OPTIONS

       -h     Print  brief  help;  includes  version number and summary of all
              options, including expert options.

       -m     Include in the alignment only those  symbols  aligned  to  match
              states.  Do not show symbols assigned to insert states.

       -o <f> Save alignment to file <f> instead of to standard output.

       -q     quiet;  suppress all output except the alignment itself.  Useful
              for piping or redirecting the output.

EXPERT OPTIONS

       --informat <s>
              Assert that the input seqfile is  in  format  <s>;  do  not  run
              Babelfish  format autodection. This increases the reliability of
              the program somewhat, because the Babelfish can  make  mistakes;
              particularly recommended for unattended, high-throughput runs of
              HMMER. Valid format strings include FASTA, GENBANK,  EMBL,  GCG,
              PIR,  STOCKHOLM, SELEX, MSF, CLUSTAL, and PHYLIP. See the User’s
              Guide for a complete list.

       --mapali <f>
              Reads an alignment from file <f>  and  aligns  it  as  a  single
              object  to  the  HMM;  e.g.  the alignment in <f> is held fixed.
              This allows you to align sequences to a model with hmmalign  and
              view  them  in  the  context  of  an  existing  trusted multiple
              alignment.  The alignment to the alignment is defined by a "map"
              kept  in the HMM, and so is fast and guaranteed to be consistent
              with the way the HMM was constructed from  the  alignment.   The
              alignment in the file <f> must be exactly the alignment that the
              HMM was built from.  Compare the --withali option.

       --oneline
              Output the alignment with one line  per  sequence,  rather  than
              interleaving   the   sequence  alignment  blocks.  Only  affects
              Stockholm format output.

       --outformat <s>
              Output the alignment in format <s>.  The  default  is  Stockholm
              format.  Valid  formats  include Stockholm, SELEX, MSF, Clustal,
              Phylip, and A2M.

       --withali <f>
              Reads an alignment from file <f>  and  aligns  it  as  a  single
              object  to  the  HMM;  e.g.  the alignment in <f> is held fixed.
              This allows you to align sequences to a model with hmmalign  and
              view  them  in  the  context  of  an  existing  trusted multiple
              alignment. The  alignment  to  the  alignment  is  done  with  a
              heuristic  (nonoptimal) dynamic programming procedure, which may
              be  somewhat  slow  and  is  not  guaranteed  to  be  completely
              consistent  with  the  way  the  HMM  was constructed (though it
              should be quite close).  However, any alignment can be used, not
              just  the  alignment  that  the  HMM was built from. Compare the
              --mapali option.

SEE ALSO

       Master man page, with full list of and  guide  to  the  individual  man
       pages: see hmmer(1).

       For  complete  documentation,  see  the  user  guide that came with the
       distribution   (Userguide.pdf);   or   see   the   HMMER   web    page,
       http://hmmer.wustl.edu/.

COPYRIGHT

       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
       Freely distributed under the GNU General Public License (GPL).
       See the file COPYING in your distribution for details on redistribution
       conditions.

AUTHOR

       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA
       http://www.genetics.wustl.edu/eddy/