Sim4
Overview
Sim4 aligns an expressed DNA sequence with a genomic sequence, allowing
for introns. Currently, five major alignment display options are supported.
Setup
To use Sim4, it is necessary to set the Sim4 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/sim4.setup.csh
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For sh and bash:
. /usr/local/setup/sim4.setup.sh
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Usage
Sim4 can be invoked using the command sim4 followed by 2 sequence file
names.
Examples
The following is an example PBS script to run a Sim4 job on LION-XE
for a maximum of 10 hours. The first sequence file is called foo.seq.
The second file is called foo_db.seq. Both files must be in FASTA file
format. Both of these files are in the directory /home/foo/sim4.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00:00
#PBS -j oe
# setup the Sim4 environment
. /usr/local/setup/sim4.setup.sh
# change the current working directory to the directory
# that contains the input files.
cd /home/foo/sim4
# run Sim4
sim4 foo.seq foo_db.seq
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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
Information on Sim4 can be found online at http://globin.cse.psu.edu/globin/html/docs/sim4.html.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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