ClustalW
Overview
ClustalW is a general purpose multiple sequence
alignment program for DNA or proteins. It produces biologically
meaningful multiple sequence alignments of divergent sequences,
calculates the best match for the selected sequences, and lines them
up so that the identities, similarities and differences can be seen.
Setup
To use ClustalW, it is necessary that the
ClustalW environment be setup.
This can be done 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/clustalw.setup.csh
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For bash and sh:
. /usr/local/setup/clustalw.setup.sh
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Usage
ClustalW is intended to be run on LION-XE and LION-XL in batch mode by
submitting a job through PBS using the -batch option to clustalw.
A sample PBS script can be found in the Examples section.
Examples
The following is an example PBS script to run ClustalW
in batch mode to align a sequence with input file
input.ext and output file
output.ext.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00:00
#PBS -j oe
# setup the ClustalW environment
. /usr/local/setup/clustalw.setup.sh
# change the current working directory to the directory
# where the input file can be found.
cd /home/foo/clustalw
# run ClustalW
clustalw -batch -infile=input.ext -outfile=output.ext
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Documentation
Documentation is available on LION-XE and LION-XL in the directory
/usr/global/clustalw in the file clustalw_help.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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