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Detail publikace
MARTÍNEK, T. LEXA, M.
Originální název
Hardware Acceleration of Approximate Palindromes Searching
Typ
článek ve sborníku ve WoS nebo Scopus
Jazyk
angličtina
Originální abstrakt
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.
Klíčová slova
Approximate palindromes, systolic array, FPGA technology
Autoři
MARTÍNEK, T.; LEXA, M.
Rok RIV
2008
Vydáno
8. 12. 2008
Nakladatel
IEEE Computer Society
Místo
Taipei
ISBN
978-1-4244-2796-3
Kniha
The International Conference on Field-Programmable Technology
Strany od
65
Strany do
72
Strany počet
8
URL
https://www.fit.vut.cz/research/publication/8780/
BibTex
@inproceedings{BUT33438, author="Tomáš {Martínek} and Matej {Lexa}", title="Hardware Acceleration of Approximate Palindromes Searching", booktitle="The International Conference on Field-Programmable Technology", year="2008", pages="65--72", publisher="IEEE Computer Society", address="Taipei", doi="10.1109/FPT.2008.4762367", isbn="978-1-4244-2796-3", url="https://www.fit.vut.cz/research/publication/8780/" }