Dotter
Overview
Dotter is a graphical dotplot program for detailed
comparison of two sequences.
Setup
To use Dotter, it is necessary to set the environment
by running a special command sequence once per login session. You may
optionally place these commands in your .cshrc (C Shell users) or .bash_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/dotter.setup.csh
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For sh and bash:
. /usr/local/setup/dotter.setup.sh
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Usage
Dotter can be invoked via the command dotter.
Examples
The following is an example PBS script to run a Dotter
job on LION-XE for a maximum of 10 hours. The query sequence input file
is called query.fa and is in fasta format. The subject
sequence input file is
called subject.fa and is in fasta format. Both files are in the
directory /home/foo/dotter.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00:00
#PBS -j oe
# setup the Dotter environment
. /usr/local/setup/dotter.setup.sh
# change the current working directory to the directory
# that contains the input files.
cd /home/foo/dotter
# run Dotter
dotter query.fa subject.fa
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Further information on PBS scripts and submitting jobs on the LION-XE
and LION-XL clusters can be found in the User Guides section of the
HPC website.
Documentation
Dotter command options can be found by running dotter with no
options or arguments.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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