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hmmalign (version 0.1.0)
Sequence should be in FASTA format
(--trim)

What it does

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

Options for Specifying the Alphabet

The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking at the composition of the msafile. Autodetection is normally quite reliable, but occasionally alphabet type may be ambiguous and autodetection can fail (for instance, on tiny toy alignments of just a few residues). To avoid this, or to increase robustness in automated analysis pipelines, you may specify the alphabet type of msafile with these options.

Attribution

This Galaxy tool relies on HMMER3 from http://hmmer.janelia.org/ Internally the software is cited as:

# hmmscan :: search sequence(s) against a profile database
# HMMER 3.1 (February 2013); http://hmmer.org/
# Copyright (C) 2011 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

The wrappers were written by Eric Rasche and is licensed under Apache2. The documentation is copied from the HMMER3 documentation.