hmme(l)

NAME

hmme
    - emit likely sequences from an HMM

SYNOPSIS
hmme [options] hmmfile

DESCRIPTION
hmme creates a set of likely sequences, according to the statistics of a given HMM. This is sometimes useful for comparing different HMMs, or just spot-checking that an HMM contains reasonable numbers (i.e., a globin HMM should produce sequences that look like globins).

By default, hmme produces 10 likely sequences and prints them to stdout in a multiple alignment format. There are options for changing the number of sequences or the format.

OPTIONS

-b  Emit the single best sequence, according to the model. "Best" is defined here as the most probable sequence. Compare the -B option.

-f  Print the sequences in FASTA (unaligned) format instead of SELEX alignment format.

-h  Print short usage and help info for the program.

-n <number>
    Generate <number> sequences instead of the default 10.

-o <outfile>
    Save the sequences in a file <outfile> rather than printing them to stdout.

-q  quiet -- suppress the verbose banner. Useful for piping the output of hmme into another program or script.

-r <rfile>
    Read the random sequence model from <rfile>. This model is used as the null hypothesis for calculating log-odds alignment scores.

-s <seed>
    Set the seed of the random number generator to <seed>. Useful for re-generating the same data sets, by giving the same seed.

-B  Generate the single best sequence. Here, "best" is defined as the highest scoring sequence, not the most probable sequence. (Recall that scoring uses a log-odds system, the probability of the sequence given the model divided by the probability of the sequence given a simple random sequence model.) The difference between -b and -B is usually minor.

SEE ALSO

Overview page: hmmer(l)

Individual man pages: hmma(l), hmmb(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