A banded smith-waterman FPGA accelerator for mercury BLASTP

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

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

28 Scopus citations

Abstract

Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. The popular BLASTP software for this task has become a bottleneck for proteomic database search. One third of this software's time is spent executing the Smith-Waterman dynamic programming algorithm. This work describes a novel FPGA design for banded Smith-Waterman, an algorithmic variant tuned to the needs of BLASTP. This design has been implemented in Mercury BLASTP, our FPGA-accelerated version of the BLASTP algorithm. We show that Mercury BLASTP runs 6-16 times faster than software BLASTP on a modern CPU while delivering 99% identical results.

Original languageEnglish
Title of host publicationProceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
Pages765-769
Number of pages5
DOIs
StatePublished - 2007
Event2007 International Conference on Field Programmable Logic and Applications, FPL - Amsterdam, Netherlands
Duration: Aug 27 2007Aug 29 2007

Publication series

NameProceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL

Conference

Conference2007 International Conference on Field Programmable Logic and Applications, FPL
Country/TerritoryNetherlands
CityAmsterdam
Period08/27/0708/29/07

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