man page(1) manual page
Table of Contents

NAME

hmm-convert
- convert HMM files from binary to ASCII, or vice versa

SYNOPSIS

hmm-convert [options] <old HMM file> <new

DESCRIPTION

hmm-convert converts between HMM file formats. Two formats are used: a binary format, and an ASCII format. The binary format is more compact but it is not always portable between different machines. The ASCII format is also advantageous for manipulating HMM files, since it is easily readable by scripts. By default, hmm-convert reads <old HMM file> and saves it in ASCII format in <new HMM file>. The -b option causes the program to create a binary file.

hmm-convert also supports conversions into GCG Profile format, via the -P option. This lets you build HMMs with the HMMER package, but use GCG software to do searches. This is used for using specialized hardware (such as the Compugen Bioccelarator) which runs GCG profiles but not HMMs. The resulting profile is only an approximation of an HMM.

OPTIONS

-b
Save the new HMM file in binary format rather than ASCII.

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

-P
Convert to a format compatible with the .prf GCG profile format.

SEE ALSO

 Overview page: hmmer(l)

Individual man pages: hmma(l), hmmb(l), hmme(l), hmmfs(l), hmmls(l), hmms(l), hmmsw(l), hmmt(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

Table of Contents