Ubuntu Manpage: hmm2align - align sequences to an HMM profile

NAME

       hmm2align - align sequences to an HMM profile

SYNOPSIS

       hmm2align [options] hmm2file seqfile

DESCRIPTION

       hmm2align  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 - hmm2align 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 hmm2align 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 hmm2align 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.

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/