Difference between revisions of "PfamScan"

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* Validated 4/5/2018

Revision as of 20:25, 5 April 2018


pfamscan website  

Search a FASTA file against a library of Pfam HMMs

Required Modules


  • 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/'.


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


  • Validated 4/5/2018