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 sequences in
seqfile are aligned in unihit local alignment mode.
Therefore they should already be known to contain a single domain; they should
not contain more than one domain. They may be fragments. 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 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.
- --allcol
- Include columns in the output alignment for every match
(consensus) state in the hmmfile, even if it means having all-gap
columns. This is useful in analysis pipelines that need to be able to
maintain a predetermined profile HMM architecture (with an unchanging
number of consensus columns) through an hmmalign step.
- --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 msafile is in format
<s>. Currently the accepted multiple alignment sequence file
formats only include Stockholm and SELEX. Default is to autodetect the
format of the file.
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 (@HMMER_URL@).
COPYRIGHT¶
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page
(@HMMER_URL@).
AUTHOR¶
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org