Acceleration of the Smith-Waterman algorithm for DNA sequence alignment using an FPGA platform

Strengholt, B.; Brobbel, M.

Acceleration of the Smith-Waterman algorithm for DNA sequence alignment using an FPGA platform

Bachelor thesis (2013)

Authors

B. Strengholt

M. Brobbel

Contributors

Z. Al-Ars (mentor)

Department

Computer Engineering

Fpga Acceleration Smith-waterman

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Published Date

02-07-2013

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Faculty

Electrical Engineering, Mathematics and Computer Science

Department

Computer Engineering

Abstract

With the sequencing of DNA becoming cheaper and the resulting stack of data growing bigger, there is a big challenge for both engineer and biologist. Researchers are limited by their computational power. In this thesis, first an overview of sequence alignment algorithms will be given. Then a method to store the values of the similarity score matrix of the Smith-Waterman algorithm differentially will be presented. And finally, a description of the system approach used to design an accelerator, which implements this method, will be given. Implementation of the system design on an Artix-7 XC7A200T-2C FPGA, could lead to a total performance of 94 GCU/s. This is a speed up of 5x compared to conventional CPUs.

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