A flexible technique for the automatic design for approximate string matching architectures

MARTÍNEK, Tomáš; Matej LEXA; Jan KOŘENEK and Otto FUČÍK. A flexible technique for the automatic design for approximate string matching architectures. In Proceedings of 2006 IEEE Design and Diagnostics of Electronic Circuits and Systems Workshop. Praha: IEEE Computer Society, 2006, p. 83-84. ISBN 1424401844.

Basic information

Original name

A flexible technique for the automatic design for approximate string matching architectures

Name in Czech

Flexibilní technika pro automatické navrhování architektur pro hledání podobnosti řetězců

Authors

MARTÍNEK, Tomáš (203 Czech Republic); Matej LEXA (703 Slovakia, guarantor); Jan KOŘENEK (203 Czech Republic) and Otto FUČÍK (203 Czech Republic)

Edition

Praha, Proceedings of 2006 IEEE Design and Diagnostics of Electronic Circuits and Systems Workshop, p. 83-84, 2 pp. 2006

Publisher

IEEE Computer Society

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Other information

Language

English

Type of outcome

Proceedings paper

Field of Study

20206 Computer hardware and architecture

Country of publisher

Czech Republic

Confidentiality degree

is not subject to a state or trade secret

RIV identification code

RIV/00216224:14330/06:00016791

Organization unit

Faculty of Informatics

ISBN

1424401844

UT WoS

000238973400021

Keywords in English

Approximate string matching; systolic array architecture; FPGA; DNA sequence analysis

Tags

Approximate string matching, DNA sequence analysis, FPGA, systolic array architecture

Tags

International impact, Reviewed

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Abstract

V originále

Systolic array architectures for approximate string matching play a significant role as hardware accelerators in biological applications. However, their wider use is limited by the lack of flexibility required by often variable tasks. In this respect, it is desirable to develop a procedure for automatic design and implementation of such accelerators to reach high performance and efficiency with as little human effort on the side of the designer as possible. This paper proposes the essential element of such procedure, a method for the calculation of generic systolic array parameters with respect to maximal performance and efficient resource utilization.

In Czech

V tomto článku navrhujeme metodu pro výpočet optimální konfigurace systolického pole pro použití v hardwarových akcelerátorech porovnávání řetězců v molekulárně-biologických aplikacích.