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Parallel Prefiltering for Accelerating HHblits on the Convey HC-1

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dc.contributor.authorBromberger, Michael
dc.contributor.authorNowak, Fabian
dc.date.accessioned2017-12-06T09:07:45Z
dc.date.available2017-12-06T09:07:45Z
dc.date.issued2013
dc.description.abstractHHblits is a bioinformatics application for finding proteins with common ancestors. To achieve more sensitivity, the protein sequences of the query are not compared directly against the database protein sequences, but rather their Hidden Markov Models are compared. Thus, HHblits is very time-consuming and therefore needs to be accelerated. A multi-FPGA system such as the Convey HC-1 is a promising candidate 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.doi10.1007/BF03354237
dc.identifier.pissn0177-0454
dc.identifier.urihttps://dl.gi.de/handle/20.500.12116/8604
dc.language.isoen
dc.publisherGesellschaft für Informatik e.V.
dc.relation.ispartofPARS: Parallel-Algorithmen, -Rechnerstrukturen und -Systemsoftware: Vol. 30, No. 1
dc.relation.ispartofseriesPARS: Parallel-Algorithmen, -Rechnerstrukturen und -Systemsoftware
dc.subjectHide Markov Model
dc.subjectViterbi Algorithm
dc.subjectMemory Controller
dc.subjectResult Matrix
dc.subjectFPGA Design
dc.titleParallel Prefiltering for Accelerating HHblits on the Convey HC-1en
dc.typeText/Journal Article
gi.citation.endPage57
gi.citation.startPage47

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