Split and Merge Functions for Supporting Multiple Processing Pipelines in Mercury BLASTN

Authors

Jwalant Ahir, Washington University in St Louis
Jeremy Buhler, Washington University in St LouisFollow
Roger D. Chamberlain, Washington University in St LouisFollow

Document Type

Technical Report

Department

Computer Science and Engineering

Publication Date

2010

Filename

WUCSE-2010-23.pdf

Technical Report Number

WUCSE-2010-23

Abstract

Biosequence similarity search is an important application in computational biology. Mercury BLASTN, an FPGA-based implementation of BLAST for DNA, is one of the alternatives for fast DNA sequence comparison. The re-design of BLAST into a streaming application combined with a high-throughput hardware pipeline have enabled Mercury BLAST to emerge as one of the fastest implementations of bio-sequence similarity search. This performance can be further enhanced by exploiting the data-level parallelism present within the application. Here we present a multiple FPGA-based Mercury BLASTN design in order to double the speed and throughput of DNA sequence computation. This paper describes a dual Mercury BLASTN design, the detailed design of the split and merge functions, and simulation results.

Comments

Permanent URL: http://dx.doi.org/10.7936/K7NC5ZDS

Recommended Citation

Ahir, Jwalant; Buhler, Jeremy; and Chamberlain, Roger D., "Split and Merge Functions for Supporting Multiple Processing Pipelines in Mercury BLASTN" Report Number: WUCSE-2010-23 (2010). All Computer Science and Engineering Research.
https://openscholarship.wustl.edu/cse_research/39