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Local Alignment Search in Genetic Sequences on a Low-Cost FPGA

Authors:
Timm Bostelmann
Thomas Fabian Starke
Sergei Sawitzki

Keywords: FPGA; BLAST; DNA; local alignment

Abstract:
The search for local alignments in genetic sequences is a common challenge in the field of bioinformatics. The problem is to find similar subsequences in genetic sequences of different lengths. Usually, the search is done in a genome database that contains hundreds of millions of sequences and rising. Due to the large amount of data, the speed is of a high concern. The search for a local alignment between a query-sequence and a database-sequence is usually done with the Basic Local Alignment Search Tool (BLAST) algorithm. In this work, an implementation of an accelerator for the BLAST algorithm on a low-cost Field-Programmable Gate Array (FPGA) is presented. The data is processed in a tree-like hardware architecture. The advantages and disadvantages of the presented approach are shown and discussed. Finally, an outlook is given on the pending issues of the current implementation. The main contribution of this paper is the focus on an implementation with support of low-cost hardware.

Pages: 39 to 43

Copyright: Copyright (c) IARIA, 2017

Publication date: September 10, 2017

Published in: conference

ISSN: 2308-426X

ISBN: 978-1-61208-585-2

Location: Rome, Italy

Dates: from September 10, 2017 to September 14, 2017