seg
Overview
seg divides sequences into contrasting segments of low-complexity
and high-complexity. Low-complexity segments defined by the
algorithm represent "simple sequences" or "compositionally-biased
regions".
Locally-optimized low-complexity segments are produced at defined
levels of stringency, based on formal definitions of local
compositional complexity. The segment lengths and the number of
segments per sequence are determined automatically by the algorithm.
The input is a FASTA-formatted sequence file, or a database file
containing many FASTA-formatted sequences. seg is tuned for amino
acid sequences.
Setup
To use seg it is necessary to set your seg 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/seg.setup.csh
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For sh and bash:
source /usr/local/setup/seg.setup.sh
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Usage
seg is invoked with the command seg.
Examples
The following is an example PBS script to run a seg job on LION-XE for a
maximum of 2 hours. The FASTA formatted input file is called input.fa and
is found in the scope of this example in /home/foo/seg. Since seg prints
its output to STDOUT (standard output), the command output will be found
in the normal PBS output file.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=2:00:00
#PBS -j oe
#PBS -q lionxe-serial
# setup the seq environment
. /usr/local/setup/seg.setup.sh
# change the current working directory to the directory where
# the input file can be found
cd /home/foo/seg
# run the seg command
seg input.fa
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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 seg can be found on LION-XE in the file
/usr/global/seg/seg.doc.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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