Difference between revisions of "PfamScan"

Revision as of 18:10, 13 February 2015

Description

pfamscan website

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 '/scratch/lfs/bio/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

@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 19: / Line 19: @@
 Search a FASTA file against a library of Pfam HMMs
-Note that on our system the pfamscan module is an alias for the [[HMMER3|hmmer]] module as we installed pfamscan within hmmer.
 <!--Modules-->
@@ Line 44: / Line 42: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+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>/scratch/lfs/bio/reference/pfam/current/</code>'.
 |}}