Detailed Information on Publication Record

MARTÍNEK, Tomáš and Matej LEXA. Hardware Acceleration of Approximate Tandem Repeat Detection. In 18th IEEE Symposium on Field-Programmable Custom Computing Machines. Los Alamitos, CA, USA: IEEE Computer Society, 2010, p. 79-86. ISBN 978-0-7695-4056-6.

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Basic information
Original name	Hardware Acceleration of Approximate Tandem Repeat Detection
Authors	MARTÍNEK, Tomáš (203 Czech Republic, guarantor) and Matej LEXA (703 Slovakia, belonging to the institution).
Edition	Los Alamitos, CA, USA, 18th IEEE Symposium on Field-Programmable Custom Computing Machines, p. 79-86, 8 pp. 2010.
Publisher	IEEE Computer Society

Other information
Original language	English
Type of outcome	Proceedings paper
Field of Study	20206 Computer hardware and architecture
Country of publisher	United States of America
Confidentiality degree	is not subject to a state or trade secret
Publication form	printed version "print"
RIV identification code	RIV/00216224:14330/10:00048631
Organization unit	Faculty of Informatics
ISBN	978-0-7695-4056-6
Keywords (in Czech)	FPGA; tandemové opakování; analýza sekvence DNA; systolické pole; dynamické programování
Keywords in English	Approximate tandem repeat; dynamic programming; systolic array; FPGA; DNA;
Tags	International impact, Reviewed
Changed by	Changed by: doc. Ing. Matej Lexa, Ph.D., učo 31298. Changed: 17/1/2013 16:44.

Abstract
Understanding the structure and function of DNA sequences represents an important area of research in modern biology. Unfortunately, analysis of such data is often complicated by the presence of mutations introduced by evolutionary processes.They increase the time-complexity of algorithms for sequence analysis by introducing an element of uncertainty, complicating their practical usage. This paper investigates the possibilities for hardware acceleration of approximate tandem repeat searching and describes a parametrized architecture suitable for chips with FPGA technology. The proposed architecture is able to detect tandems with both types of errors (mismatches and indels) and does not limit the length of detected tandem. A prototype of the circuit was implemented in VHDL language and synthesized for Virtex5 technology. Application on test sequences shows that the circuit is able to speed up tandem searching in orders of thousands in comparison with the best-known software method relying on suffix arrays.

Abstract

Understanding the structure and function of DNA sequences represents an important area of research in modern biology. Unfortunately, analysis of such data is often complicated by the presence of mutations introduced by evolutionary processes.They increase the time-complexity of algorithms for sequence analysis by introducing an element of uncertainty, complicating their practical usage. This paper investigates the possibilities for hardware acceleration of approximate tandem repeat searching and describes a parametrized architecture suitable for chips with FPGA technology. The proposed architecture is able to detect tandems with both types of errors (mismatches and indels) and does not limit the length of detected tandem. A prototype of the circuit was implemented in VHDL language and synthesized for Virtex5 technology. Application on test sequences shows that the circuit is able to speed up tandem searching in orders of thousands in comparison with the best-known software method relying on suffix arrays.

Abstract (in Czech)
Prezentujeme algoritmus pro vyhledavani pribliznych tandemovych opakovani v biologickych sekvencich. Algoritmus je implementovan na FPGA cipech.

Links
GA204/08/1560, research and development project	Name: Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA
GA204/08/1560, research and development project	Investor: Czech Science Foundation, In vitro and in silico identification of non-canonical DNA structures in genomic sequences