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Accelerating Charged Single alpha-helix Detection on FPGA

Authors:
Sam Khozama
Zoltán Nagy
Zoltán Gáspári

Keywords: FPGA; FT_CHARGE; CSAH; Charged Single alpha-helix; Hardware acceleration.

Abstract:
Novel biological sequences are determined at an extreme pace producing a huge amount of data each day. Implementing and speeding up the bioinformatics algorithms, which need very fast and accurate results, is the main advantage of reconfigurable architectures like Field-Programmable Gate Array (FPGA), in addition to the low precision input data for these kinds of algorithms, which can be stored in 2-5 bits. Detecting structural motifs such as Charged Single alpha-Helixes (CSAH) is a computationally intensive task which can be accelerated by using FPGA. The goal of our research is to further improve the processing speed of our algorithm called FT_CHARGE to analyze large databases in a reasonable time. Using the largest state-of-the-art FPGA devices, either the number of processing units or the parallelism inside the processing units can be increased. In this paper, we provide details and compare the two design approaches in terms of speed, implementation and accuracy. We propose a new architecture that can perform search for CSAH 32 times faster compared to our previous FPGA implementation.

Pages: 16 to 19

Copyright: Copyright (c) IARIA, 2020

Publication date: September 27, 2020

Published in: conference

ISSN: 2308-4383

ISBN: 978-1-61208-792-4

Location: Lisbon, Portugal

Dates: from September 27, 2020 to October 1, 2020