Single pass streaming BLAST on FPGAs

Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating th...

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Bibliographic Details
Published in:Parallel computing Vol. 33; no. 10; pp. 741 - 756
Main Authors: Herbordt, Martin C., Model, Josh, Sukhwani, Bharat, Gu, Yongfeng, VanCourt, Tom
Format: Journal Article
Language:English
Published: Netherlands Elsevier B.V 01.11.2007
Subjects:
Bioinformatics
Computational accelerators
Configurable computing
High performance computing
Configurable computing
High performance computing
Computational accelerators
Bioinformatics
ISSN:0167-8191, 1872-7336
Online Access:Get full text
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Summary:Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST.
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content type line 23
Now at the MIT Lincoln Laboratory.
Now at Altera Corporation
ISSN:0167-8191
1872-7336
DOI:10.1016/j.parco.2007.09.003