NAME
SYNOPSIS hmma [options] hmmfile seqfile DESCRIPTION hmma makes a multiple sequence alignment of the sequences in seqfile, using the trained hidden Markov model in hmmfile.
seqfile may contain RNA, DNA, or amino acid sequences (don't mix them, though). It may be in any one of several different common sequence file formats, including EMBL, Genbank, and FASTA. The easiest to type in yourself is FASTA format, which consists of a line starting with > containing the name (one word) and an optional description of the sequence, followed by one or more lines of sequence.
The multiple sequence alignment is printed on the terminal screen; to save it, one must either redirect output to a file or use the -o option.
The alignment contains both upper-case and lower-case amino acids. Upper-case amino acids are aligned to match states in the HMM. Lower-case amino acids were assigned to insert states. An HMM does not attempt to align inserts. Contiguous inserts of greater than 1 residue are simply printed left-justified, with no gaps.
OPTIONS
AUTHOR Sean Eddy (eddy@genetics.wustl.edu) SEE ALSO
Overview: hmmer(l)
Individual man pages: hmmb(l), hmme(l), hmmfs(l), hmmls(l), hmms(l), hmmsw(l), hmmt(l), hmm-convert(l)
User guide and tutorial: Userguide.ps BUGS No major bugs known.
Not very tolerant of errors on the command line.
NOTES
This software and documentation is Copyright (C) 1992-1995, Sean R. Eddy. It is freely distributable under terms of the GNU General Public License. See COPYING, in the source code distribution, for more details, or contact me.
Sean Eddy Dept. of Genetics, Washington Univ. School of Medicine 660 S. Euclid Box 8232 St Louis, MO 63110 USA Phone: 1-314-362-7666 FAX : 1-314-362-2985 Email: eddy@genetics.wustl.edu