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Scalable hardware accelerator for comparing DNA and protein sequences

Authors:

Yves Van de PeerAuthors Info & Claims

InfoScale '06: Proceedings of the 1st international conference on Scalable information systems

Pages 33 - es

https://doi.org/10.1145/1146847.1146880

Published: 30 May 2006 Publication History

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Abstract

Comparing genetic sequences is a well-known problem in bioinformatics. Newly determined sequences are being compared to known sequences stored in databases in order to investigate biological functions. In recent years the number of available sequences has increased exponentially. Because of this explosion a speedup in the comparison process is highly required. To meet this demand we implemented a dynamic programming algorithm for sequence alignment on reconfigurable hardware. The algorithm we implemented, Smith-Waterman-Gotoh (SWG) has not been implemented in hardware before. We show a speedup factor of 40 in a design that scales well with the size of the available hardware. We also demonstrate the limits of larger hardware for small problems, and project our design on the largest Field Programmable Gate Array (FPGA) available today.

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Koliogeorgi KXydis SGaydadjiev GSoudris D(2022)GANDAFL: Dataflow Acceleration for Short Read Alignment on NGS DataIEEE Transactions on Computers10.1109/TC.2022.314411571:11(3018-3031)Online publication date: 1-Nov-2022
https://doi.org/10.1109/TC.2022.3144115
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Scalable hardware accelerator for comparing DNA and protein sequences

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Published In

InfoScale '06: Proceedings of the 1st international conference on Scalable information systems

May 2006

512 pages

ISBN:1595934286

DOI:10.1145/1146847

General Chair:
Xiaohua Jia
City University of Hong Kong

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

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Published: 30 May 2006

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InfoScale '06 Paper Acceptance Rate 33 of 91 submissions, 36%;

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Liang DThomaz E(2019)Audio-Based Activities of Daily Living (ADL) Recognition with Large-Scale Acoustic Embeddings from Online VideosProceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies10.1145/33144043:1(1-18)Online publication date: 29-Mar-2019
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Guo LLau JRuan ZWei PCong J(2019)Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: A Race Between FPGA and GPU2019 IEEE 27th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM)10.1109/FCCM.2019.00027(127-135)Online publication date: Apr-2019
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A hardware accelerator for the alignment of multiple DNA sequences

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