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FCCM
2006
IEEE

Single Pass, BLAST-Like, Approximate String Matching on FPGAs

9 years 7 months ago
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
Abstract: 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 contributions are two new algorithms for emulating the seeding and extension phases of BLAST. These operate in a single pass through a database at streaming rate (110 Maa/sec on a VP70 for query sizes up to 600 and 170 Maa/sec on a Virtex4 for query sizes up to 1024), and with no preprocessing other than loading the query string. Further, they use very high 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.
Martin C. Herbordt, Josh Model, Yongfeng Gu, Bhara
Added 11 Jun 2010
Updated 11 Jun 2010
Type Conference
Year 2006
Where FCCM
Authors Martin C. Herbordt, Josh Model, Yongfeng Gu, Bharat Sukhwani, Tom Van Court
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