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/