Difference between revisions of "PfamScan"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|pfamscan}} |{{#vardefine:url|http://ftp.ebi.ac.uk/pub/...") |
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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Search a FASTA file against a library of Pfam HMMs | Search a FASTA file against a library of Pfam HMMs | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | On our system the pfamscan module is an alias for the [[HMMER3|hmmer]] module as we installed pfamscan within hmmer. | |
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| + | 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>'. | ||
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Revision as of 18:10, 13 February 2015
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 '/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