Difference between revisions of "PfamScan"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| Line 34: | Line 34: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:22, 6 December 2019
Description
Search a FASTA file against a library of Pfam HMMs
Required Modules
Serial
- pfamscan
System Variables
- HPC_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