Preliminary results in accelerating profile HMM search on FPGAs

Arpith C. Jacob, Joseph M. Lancaster, Jeremy D. Buhler, Roger D. Chamberlain

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

15 Scopus citations

Abstract

Comparison between biosequences and probabilistic models is an increasingly important part of modern DNA and protein sequence analysis. The large and growing number of such models in today's databases demands computational approaches to searching these databases faster, while maintaining high sensitivity to biologically meaningful similarities. This work1 describes an FPGA-based accelerator for comparing proteins to Hidden Markov Models of the type used to represent protein motifs in the popular HMMER motif finder. Our engine combines a systolic array design with enhancements to pipeline the complex Viterbi calculation that forms the core of the comparison, and to support coarse-grained parallelism and streaming of multiple sequences within one FPGA. Performance estimates based on a functioning VHDL realisation of our design show a 190x speedup over the same computation in optimised software on a modern general-purpose CPU.

Original languageEnglish
Title of host publicationProceedings - 21st International Parallel and Distributed Processing Symposium, IPDPS 2007; Abstracts and CD-ROM
DOIs
StatePublished - 2007
Event21st International Parallel and Distributed Processing Symposium, IPDPS 2007 - Long Beach, CA, United States
Duration: Mar 26 2007Mar 30 2007

Publication series

NameProceedings - 21st International Parallel and Distributed Processing Symposium, IPDPS 2007; Abstracts and CD-ROM

Conference

Conference21st International Parallel and Distributed Processing Symposium, IPDPS 2007
Country/TerritoryUnited States
CityLong Beach, CA
Period03/26/0703/30/07

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