CISTER
Overview
Cister predicts regulatory regions in DNA sequences by searching for
clusters of cis-elements.
Setup
To use Cister it is necessary to set your Cister 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/cister.setup.csh
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For sh and bash:
. /usr/local/setup/cister.setup.sh
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Usage
Cister is invoked with the command cister.
Examples
The following is an example PBS script to run a cister 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/cister. There are two output files:
clusterout, which contains information about predicted cluster locations, and
motifout, which contains information about predicted cis-element locations.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00:00
#PBS -j oe
#PBS -q lionxe-serial
# setup the Cister environment
. /usr/local/setup/cister.setup.sh
# change the current working directory to the directory where
# the input file and matrix file can be found
cd /home/foo/cister
# run the cister command
cister -i myseqs.fa -m mymatrices -c clusterout -o motifout
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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 cister command options and syntax can be found on the
command-line cister page at http://zlab.bu.edu/~mfrith/cister_download.html
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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