Parallel Prefiltering for Accelerating HHblits on the Convey HC-1
| dc.contributor.author | Bromberger, Michael | |
| dc.contributor.author | Nowak, Fabian | |
| dc.date.accessioned | 2017-06-29T21:44:19Z | |
| dc.date.available | 2017-06-29T21:44:19Z | |
| dc.date.issued | 2013 | |
| dc.description.abstract | HHblits is a bioinformatics application for finding proteins with common ances- tors. To achieve more sensitivitythe protein sequences of the query are not compared directly against the database protein sequencesbut rather their Hidden Markov Models are compared. ThusHHblits is very time-consuming and therefore needs to be accelerated. A multi-FPGA system such as the Convey HC-1 is a promising candiate to achieve acceleration. We present the design and implementation of a parallel coprocessor on the Convey HC-1 to accelerate HHblits after analyzing the application toward acceleration candidates. We achieve a speedup of 117.5× against a sequential implementation for FPGA-suitable data sizes per kernel and negligible speedup for the entire uniprot20 protein database against an optimized SSE implementation. | en |
| dc.identifier.pissn | 0177-0454 | |
| dc.language.iso | en | |
| dc.publisher | Gesellschaft für Informatik e.V., Fachgruppe PARS | |
| dc.relation.ispartof | PARS-Mitteilungen: Vol. 30, Nr. 1 | |
| dc.title | Parallel Prefiltering for Accelerating HHblits on the Convey HC-1 | en |
| dc.type | Text/Journal Article | |
| gi.citation.publisherPlace | Berlin |
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