Difference between revisions of "SNAP-HMM 2016"
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== Introduction == | == Introduction == | ||
SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. | SNAP-HMM is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. | ||
== Installed | == Installed Version == | ||
Although the program is actually only called SNAP, it was installed with the suffix '-HMM' to distinguish it from the [https://wiki.hpcuser.uni-oldenburg.de/index.php?title=SNAP_2016 other SNAP version]. | Although the program is actually only called SNAP, it was installed with the suffix '-HMM' to distinguish it from the [https://wiki.hpcuser.uni-oldenburg.de/index.php?title=SNAP_2016 other SNAP version]. | ||
You can find both version by typing in | You can find both version by typing in | ||
module spider snap | module spider snap | ||
The | The following versions of SNAP'''-HMM''' are installed and currently available... <br/> | ||
module load hpc-env/ | |||
... on environment ''hpc-env/8.3'': | |||
*'''SNAP-HMM/20190603'''-GCC-8.3.0 | |||
... on environment ''hpc-env/6.4'': | |||
*'''SNAP-HMM/2013-11-29'''-GCCcore-6.4.0 | |||
To load the desired version of the module, use the ''module load'' command, e.g. | |||
module load hpc-env/8.3 | |||
module load SNAP-HMM | module load SNAP-HMM | ||
== Using SNAP-HMM == | == Using SNAP-HMM == | ||
To work with the data included in SNAP-HMM, you shold use the environment variable ''$EBROOTSNAPMINHMM'' which leads to the softwares' directory: | |||
You can proceed according to the scheme ''snap <command>'' | |||
Eg.: | Eg.: | ||
snap HMM/thale DNA/thale.dna.gz | snap $EBROOTSNAPMINHMM/HMM/thale $EBROOTSNAPMINHMM/DNA/thale.dna.gz | ||
snap HMM/worm DNA/worm.dna.gz | snap $EBROOTSNAPMINHMM/HMM/worm $EBROOTSNAPMINHMM/DNA/worm.dna.gz | ||
== Documentation == | == Documentation == | ||
For further information consult the [https://github.com/KorfLab/SNAP/blob/master/README.md readme file] or visit the [http://korflab.ucdavis.edu/ developer's website]. | For further information consult the [https://github.com/KorfLab/SNAP/blob/master/README.md readme file] or visit the [http://korflab.ucdavis.edu/ developer's website]. | ||
Latest revision as of 13:02, 25 March 2021
Introduction
SNAP-HMM is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.
Installed Version
Although the program is actually only called SNAP, it was installed with the suffix '-HMM' to distinguish it from the other SNAP version. You can find both version by typing in
module spider snap
The following versions of SNAP-HMM are installed and currently available...
... on environment hpc-env/8.3:
- SNAP-HMM/20190603-GCC-8.3.0
... on environment hpc-env/6.4:
- SNAP-HMM/2013-11-29-GCCcore-6.4.0
To load the desired version of the module, use the module load command, e.g.
module load hpc-env/8.3 module load SNAP-HMM
Using SNAP-HMM
To work with the data included in SNAP-HMM, you shold use the environment variable $EBROOTSNAPMINHMM which leads to the softwares' directory:
You can proceed according to the scheme snap <command>
Eg.:
snap $EBROOTSNAPMINHMM/HMM/thale $EBROOTSNAPMINHMM/DNA/thale.dna.gz snap $EBROOTSNAPMINHMM/HMM/worm $EBROOTSNAPMINHMM/DNA/worm.dna.gz
Documentation
For further information consult the readme file or visit the developer's website.
