COMET
Overview
COMET stands for Cluster Of Motifs E-value Tool. It finds statistically
significant clusters of motifs in a DNA sequence. The motifs are
represented using 4 x L matrices which record the frequencies of the
nucleotides A, C, G, and T at each position in the motif.
Setup
To use COMET it is necessary to set your COMET 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.
|
For csh and tcsh:
source /usr/local/setup/comet.setup.csh
|
|
|
For sh and bash:
. /usr/local/setup/comet.setup.sh
|
|
Usage
COMET is invoked with the command comet.
Examples
The following is an example PBS script to run a COMET job on LION-XE for
a maximum of 10 hours. The input file is called myseqs.fa and is in FASTA
format. The matrix file is called mymatrices. Both myseqs.fa and mymatrices
are in the directory /home/foo/comet. The output file is specified as
comet.out.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00:00
#PBS -j oe
#PBS -q lionxe-serial
# setup the comet environment
. /usr/local/setup/comet.setup.sh
# change the current working directory to the directory where
# the input file and matrix file can be found
cd /home/foo/comet
# run the comet command
comet -i myseqs.fa -m mymatrices -o comet.out
|
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 COMET command options and syntax can be found on the
command-line COMET page at
http://zlab.bu.edu/~mfrith/comet/comet_download.html
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
|
