NAME¶
hmmalign - align sequences to a profile HMM
SYNOPSIS¶
hmmalign [options] <hmmfile> <seqfile>
DESCRIPTION¶
Perform a multiple sequence alignment of all the sequences in
<seqfile> by aligning them individually to the profile HMM in
<hmmfile>. The new alignment is output to
stdout in
Stockholm format.
The
<hmmfile> should contain only a single profile. If it contains
more, only the first profile in the file will be used.
Either
<hmmfile> or
<seqfile> (but not both) may be
'-' (dash), which means reading this input from
stdin rather than a
file.
The sequences in
<seqfile> are aligned in unihit local alignment
mode. Therefore they should already be known to contain only a single domain
(or a fragment of one). The optimal alignment may assign some residues as
nonhomologous (N and C states), in which case these residues are still
included in the resulting alignment, but shoved to the outer edges. To trim
these unaligned nonhomologous residues from the result, see the
--trim
option.
OPTIONS¶
- -h
- Help; print a brief reminder of command line usage and all available
options.
- -o <f>
- Direct the output alignment to file <f>, rather than to
stdout.
- --mapali <f>
- Merge the existing alignment in file <f> into the result,
where <f> is exactly the same alignment that was used to
build the model in <hmmfile>. This is done using a map of
alignment columns to consensus profile positions that is stored in the
<hmmfile>. The multiple alignment in <f> will be
exactly reproduced in its consensus columns (as defined by the profile),
but the displayed alignment in insert columns may be altered, because
insertions relative to a profile are considered by convention to be
unaligned data.
- --trim
- Trim nonhomologous residues (assigned to N and C states in the optimal
alignments) from the resulting multiple alignment output.
- --amino
- Specify that all sequences in <seqfile> are proteins. By
default, alphabet type is autodetected from looking at the residue
composition.
- --dna
- Specify that all sequences in <seqfile> are DNAs.
- --rna
- Specify that all sequences in <seqfile> are RNAs.
- --informat <s>
- Declare that the input <seqfile> is in format
<s>. Accepted sequence file formats include FASTA, EMBL,
GenBank, DDBJ, UniProt, Stockholm, and SELEX. Default is to autodetect the
format of the file.
- --outformat <s>
- Specify that the output multiple alignment is in format <s>.
Currently the accepted multiple alignment sequence file formats only
include Stockholm and SELEX.
SEE ALSO¶
See
hmmer(1) for a master man page with a list of all the individual man
pages for programs in the HMMER package.
For complete documentation, see the user guide that came with your HMMER
distribution (Userguide.pdf); or see the HMMER web page ().
COPYRIGHT¶
Copyright (C) 2013 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page ().
AUTHOR¶
The Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org
