Conference paper

MARTÍNEK Tomáš, LEXA Matej, BECK Patrik and FUČÍK Otto. Automatic Generation of Circuits for Approximate String Matching. In: 2007 IEEE Design and Diagnostics of Electronic Circuits and Systems. Krakow: IEEE Computer Society, 2007, pp. 203-208. ISBN 1-4244-1161-0.
Publication language:english
Original title:Automatic Generation of Circuits for Approximate String Matching
Title (cs):Automatické generování obvodů pro hledání podobnosti v řetězcích
Pages:203-208
Proceedings:2007 IEEE Design and Diagnostics of Electronic Circuits and Systems
Conference:The 10th IEEE Workshop on Design and Diagnostics of Electronic Circuits and Systems
Place:Krakow, PL
Year:2007
ISBN:1-4244-1161-0
Publisher:IEEE Computer Society
Keywords
automated design, approximate string matching, generic systolic array architecture, FPGA
Annotation
Hardware accelerators for approximate string matching  play an important role in an increasing number of modern bioinformatic applications. They are able to reduce the task complexity from quadratic to linear and show a speed up in orders of hundreds when compared with the respective software implementation. However, their wider use is limited by the lack of flexibility and modularity 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 typical for strongly optimized architectures, with as little human effort on the side of the designer as possible. This paper proposes the essential element of such a procedure, a method for the calculation of generic hardware architecture parameters. The proposed method is evaluated on a range of typical approximate string matching tasks. It demonstrates the differences in the designed architecture, when performance of individual tasks is maximized.
BibTeX:
@INPROCEEDINGS{
   author = {Tom{\'{a}}{\v{s}} Mart{\'{i}}nek and Matej Lexa and Patrik
	Beck and Otto Fu{\v{c}}{\'{i}}k},
   title = {Automatic Generation of Circuits for Approximate String
	Matching},
   pages = {203--208},
   booktitle = {2007 IEEE Design and Diagnostics of Electronic Circuits and
	Systems},
   year = {2007},
   location = {Krakow, PL},
   publisher = {IEEE Computer Society},
   ISBN = {1-4244-1161-0},
   language = {english},
   url = {http://www.fit.vutbr.cz/research/view_pub.php?id=8304}
}

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