Difference between revisions of "PfamScan"
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On our system the pfamscan module is an alias for the [[HMMER3|hmmer]] module as we installed pfamscan within hmmer. | On our system the pfamscan module is an alias for the [[HMMER3|hmmer]] module as we installed pfamscan within hmmer. | ||
| − | You don't have to provide the '-dir' argument to the pfam_scan.pl command as we configured it to use the default location of the most current Pfam reference data release at '<code>/ | + | You don't have to provide the '-dir' argument to the pfam_scan.pl command as we configured it to use the default location of the most current Pfam reference data release at '<code>/ufrc/data/reference/reference/pfam/current/</code>'. |
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Revision as of 15:33, 20 April 2018
Description
Search a FASTA file against a library of Pfam HMMs
Required Modules
Serial
- pfamscan
System Variables
- HPC_{{#uppercase:pfamscan}}_DIR - installation directory
Additional Information
On our system the pfamscan module is an alias for the hmmer module as we installed pfamscan within hmmer.
You don't have to provide the '-dir' argument to the pfam_scan.pl command as we configured it to use the default location of the most current Pfam reference data release at '/ufrc/data/reference/reference/pfam/current/'.
Citation
If you publish research that uses pfamscan you have to cite it as follows:
The Pfam protein families database: R.D. Finn, A. Bateman, J. Clements, P. Coggill, R.Y. Eberhardt, S.R. Eddy, A. Heger, K. Hetherington, L. Holm, J. Mistry, E.L.L. Sonnhammer, J. Tate, M. Punta Nucleic Acids Research (2014) Database Issue 42:D222-D230
Validation
- Validated 4/5/2018