MZEF
Overview
MZEF (Michael Zhang's Exon Finder) is an internal coding exon prediction
program. It starts with a potential exon and then calculates its posterior
exon probability. If the probability P > 1/2, it will be output as a
predicted exon.
Setup
To use MZEF it is necessary to set your MZEF 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/mzef.setup.csh
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For sh and bash:
. /usr/local/setup/mzef.setup.sh
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Usage
MZEF is invoked with the command mzef. This is the human version of
MZEF.
Examples
The following is an example PBS script to run a MZEF job on LION-XE for a
maximum of 2 hours. The input file is a FASTA formatted file called input.fa
found in the scope of this example in /home/foo/mzef. Output is collected 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 MZEF environment
. /usr/local/setup/mzef.setup.sh
# change the current working directory to the directory where
# the input file input.fa can be found
cd /home/foo/mzef
# run the MZEF command
mzef 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 MZEF can be found on LION-XE in the file
/usr/global/mzef/README.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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