Large-Scale Profile-HMM on the Grid Laurent Falquet Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland Borrowed from Heinz Stockinger June 17, 2006. Outline. Computing intensive sequence alignment Mapping the problem to the Grid Prototype implementation & results.
on the Grid
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
Borrowed from Heinz Stockinger
June 17, 2006
Store files on SE
Get files from SE
wg on Local Site
wg on Remote Site
Usage: wg <hmmFile> <seqFile> [options]
<hmmFile> path of the profile-HMM file containing 1 or more profiles.
<seqFile> path of the sequence file containing 1 or more sequences.
The following options are available:
-p <no> number of parallel jobs submitted to the Grid.
-r used for a remote execution of the program.
-h print this help message.
-s retrieve all status information of submitted jobs.
-v verbose: print debug messages.
-O do not retrieve the job output but only display status.
-P use pfsearch (default).
-H use hmmsearch.
Work done by Heinz Stockinger in co-operation with Marco Pagni, Lorenzo Cerutti
and Laurent Falquet
The EMBRACE project is funded by the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology for health,"contract number LHSG-CT-2004-512092.