Single pass streaming BLAST on FPGAs

Authors:
Martin C. Herbordt;Josh Model;Bharat Sukhwani;Yongfeng Gu;Tom VanCourt
Affiliations:
Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, United States;Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, United States;Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, United States;Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, United States;Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, United States
Venue:
Parallel Computing
Year:
2007

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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 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.