HMMgene
Overview
HMMgene is a program for prediction of genes in anonymous DNA. It predicts
whole genes so the predicited exons always splice correctly. It can predict
several whole or partial genes in one sequence so it can be used on whole
cosmis or even longer sequences. HMMgene can also be used to predict
splice sites and start/stop codons. If some features of a sequence are
known, such as hits to ESTs, proteins, or repeat elements, these regions
can be locked as coding or non-coding and then the program will find the
best gene structure under those conditions.
Setup
To use HMMgene it is necessary to set your HMMgene environment by running
a special command sequence once per login session. You may optionally
place these commands in your .cshrc (C Shell users) or .profile (Bourne
Shell users) to avoid having to manually run these commands on login.
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For csh and tcsh:
source /usr/local/setup/hmmgene.setup.csh
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For sh and bash:
. /usr/local/setup/hmmgene.setup.sh
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Usage
HMMgene is invoked with the command hmmgene. It takes as input a file
containing one of more DNA sequences in FASTA format. Its output is a
prediction of partial or complete genes in GFF format.
Examples
The following is an example PBS script to run a HMMgene job on LION-XE for a
maximum of 2 hours. The input is a FASTA formatted file called input.fa and
in the scope of this example is found in /home/foo/hmmgene. Output will be
in the standard PBS output file.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=2:00:00
#PBS -j oe
#PBS -q lionxe-serial
# setup the HMMgene environment
. /usr/local/setup/hmmgene.setup.sh
# change the current working directory to the directory where
# the input file can be found
cd /home/foo/hmmgene
# run the HMMgene command
hmmgene input.fa
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Further information on PBS scripts and submitting jobs on the LION-XE cluster
can be found in the User Guides section of the HPC website.
Documentation
Information on HMMgene can be found on LION-XE in the file
/usr/global/hmmgene/hmmgene1_1.ps.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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