Publication detail

Hardware Acceleration of Approximate Palindromes Searching

MARTÍNEK, T. LEXA, M.

Original Title

Hardware Acceleration of Approximate Palindromes Searching

Type

conference paper

Language

English

Original 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.

Keywords

Approximate palindromes, systolic array, FPGA technology

Authors

MARTÍNEK, T.; LEXA, M.

RIV year

2008

Released

8. 12. 2008

Publisher

IEEE Computer Society

Location

Taipei

ISBN

978-1-4244-2796-3

Book

The International Conference on Field-Programmable Technology

Pages from

65

Pages to

72

Pages count

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/"
}