Faculty of Information Technology, BUT

Publication Details

Hardware Acceleration of Approximate Palindromes Searching

MARTÍNEK Tomáš and LEXA Matej. Hardware Acceleration of Approximate Palindromes Searching. In: The International Conference on Field-Programmable Technology. Taipei: IEEE Computer Society, 2008, pp. 65-72. ISBN 978-1-4244-2796-3.
Czech title
Hardwarová akcelerace algoritmů pro vyhledávání palindromů na základě podobnosti
Type
conference paper
Language
english
Authors
Martínek Tomáš, Ing. (FIT BUT)
Lexa Matej, Ing., Ph.D. (DCSY FIT BUT)
Keywords
Approximate palindromes, systolic array, FPGA technology
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. One class of such algorithms has been designed to search for palindromes with possible errors---approximate palindromes. The best state-of-the-art methods implemented in software show time-complexity between linear and quadratic, depending on required input parameters. This paper investigates the possibilities for hardware acceleration of approximate palindrome searching and describes a parametrized architecture suitable for chips with FPGA technology. A prototype of the proposed architecture was implemented in VHDL language and synthesized for Virtex technology. Application on test sequences shows that the circuit is able to speed up palindrome searching by up to 8000x in comparison with the best-known software method relying on suffix arrays.
Published
2008
Pages
65-72
Proceedings
The International Conference on Field-Programmable Technology
Conference
The International Conference on Field-Programmable Technology, Taipei, TW
ISBN
978-1-4244-2796-3
Publisher
IEEE Computer Society
Place
Taipei, TW
DOI
BibTeX
@INPROCEEDINGS{FITPUB8780,
   author = "Tom\'{a}\v{s} Mart\'{i}nek and Matej Lexa",
   title = "Hardware Acceleration of Approximate Palindromes Searching",
   pages = "65--72",
   booktitle = "The International Conference on Field-Programmable Technology",
   year = 2008,
   location = "Taipei, TW",
   publisher = "IEEE Computer Society",
   ISBN = "978-1-4244-2796-3",
   doi = "10.1109/FPT.2008.4762367",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/8780"
}
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