PfamScan

Description

pfamscan website

PfamScan is used to search a FASTA sequence against a library of Pfam HMM

Environment Modules

Run module spider pfamscan to find out what environment modules are available for this application.

Environment Variables

Additional Usage Information

On our system the pfamscan module is an alias for the hmmer module as we installed pfamscan within hmmer. Please see https://docs.rc.ufl.edu/software/apps/hmmer/ for more information.

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 /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

Categories

biology, genomics