A banded smith-waterman FPGA accelerator for mercury BLASTP

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

doi:10.1109/FPL.2007.4380764

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 proceeding › Conference contribution › peer-review

30 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 language	English
Title of host publication	Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
Pages	765-769
Number of pages	5
DOIs	https://doi.org/10.1109/FPL.2007.4380764
State	Published - 2007
Event	2007 International Conference on Field Programmable Logic and Applications, FPL - Amsterdam, Netherlands Duration: Aug 27 2007 → Aug 29 2007

Publication series

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

Conference

Conference	2007 International Conference on Field Programmable Logic and Applications, FPL
Country/Territory	Netherlands
City	Amsterdam
Period	08/27/07 → 08/29/07

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10.1109/FPL.2007.4380764

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Harris, B., Jacob, A. C., Lancaster, J. M., Buhler, J., & Chamberlain, R. D. (2007). A banded smith-waterman FPGA accelerator for mercury BLASTP. In Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL (pp. 765-769). Article 4380764 (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL). https://doi.org/10.1109/FPL.2007.4380764

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title = "A banded smith-waterman FPGA accelerator for mercury BLASTP",

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.",

author = "Brandon Harris and Jacob, {Arpith C.} and Lancaster, {Joseph M.} and Jeremy Buhler and Chamberlain, {Roger D.}",

year = "2007",

doi = "10.1109/FPL.2007.4380764",

language = "English",

isbn = "1424410606",

series = "Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL",

pages = "765--769",

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note = "2007 International Conference on Field Programmable Logic and Applications, FPL ; Conference date: 27-08-2007 Through 29-08-2007",

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Harris, B, Jacob, AC, Lancaster, JM, Buhler, J & Chamberlain, RD 2007, A banded smith-waterman FPGA accelerator for mercury BLASTP. in Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL., 4380764, Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL, pp. 765-769, 2007 International Conference on Field Programmable Logic and Applications, FPL, Amsterdam, Netherlands, 08/27/07. https://doi.org/10.1109/FPL.2007.4380764

A banded smith-waterman FPGA accelerator for mercury BLASTP. / Harris, Brandon; Jacob, Arpith C.; Lancaster, Joseph M. et al.
Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. p. 765-769 4380764 (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AB - 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.

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Harris B, Jacob AC, Lancaster JM, Buhler J, Chamberlain RD. A banded smith-waterman FPGA accelerator for mercury BLASTP. In Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. p. 765-769. 4380764. (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL). doi: 10.1109/FPL.2007.4380764

A banded smith-waterman FPGA accelerator for mercury BLASTP

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