Single Pass, BLAST-Like, Approximate String Matching 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 contributions are two new algorithms for emulat...

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Bibliographic Details
Published in:FCCM 2006 : 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines : proceedings : 24-26 April, 2006, Napa, California pp. 217 - 226
Main Authors: Herbordt, J.C., Model, J., Yongfeng Gu, Sukhwani, B., VanCourt, T.
Format: Conference Proceeding
Language:English
Published: IEEE 01.04.2006
Subjects:
Acceleration
Bioinformatics
Data mining
DNA
Field programmable gate arrays
Genetic mutations
Hardware
Proteins
Sequences
ISBN:9780769526614, 0769526616
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 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
ISBN:9780769526614
0769526616
DOI:10.1109/FCCM.2006.64