hmm2align [options] hmm2file
seqfile
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).
- -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.
- --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.
Master man page, with full list of and guide to the individual man
pages: see hmmer2(1).
For complete documentation, see the user guide
(ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the
HMMER web page, http://hmmer.janelia.org/.
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.
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/