Publication detail

Architecture model for approximate palindrome detection

MARTÍNEK, T. LEXA, M. VOŽENÍLEK, J.

Original Title

Architecture model for approximate palindrome detection

English Title

Architecture model for approximate palindrome detection

Type

conference paper

Language

en

Original Abstract

Understanding the structure and function of DNA sequences represents an important area of research in modern biology. One of the interesting structures occurring in DNA is a palindrome. Biologists believe that palindromes play an important role in regulation of gene activity and other cell processes because they are often observed near promoters, introns and specific untranslated regions. Unfortunately, the time complexity of algorithms for palindrome detection increases when mutations in the form of character insertions, deletions or substitutions are taken into consideration. In recent years, several works have been aimed at acceleration of such algorithms using dedicated circuits capable of potentially large-scale searching. However, widespread use of such circuits is often complicated by varying user task details or the need to use a specific target platform. The objective of this work is therefore to create a model of hardware architecture for approximate palindrome detection and develop a technique for automatic mapping of this model to the target platform without intervention of an experienced designer. The proposed model and the mapping technique are implemented and evaluated on a family of chips with Virtex5 technology.

English abstract

Understanding the structure and function of DNA sequences represents an important area of research in modern biology. One of the interesting structures occurring in DNA is a palindrome. Biologists believe that palindromes play an important role in regulation of gene activity and other cell processes because they are often observed near promoters, introns and specific untranslated regions. Unfortunately, the time complexity of algorithms for palindrome detection increases when mutations in the form of character insertions, deletions or substitutions are taken into consideration. In recent years, several works have been aimed at acceleration of such algorithms using dedicated circuits capable of potentially large-scale searching. However, widespread use of such circuits is often complicated by varying user task details or the need to use a specific target platform. The objective of this work is therefore to create a model of hardware architecture for approximate palindrome detection and develop a technique for automatic mapping of this model to the target platform without intervention of an experienced designer. The proposed model and the mapping technique are implemented and evaluated on a family of chips with Virtex5 technology.

Keywords

approximate palindrome detection, architecture model, Virtex5, FPGA

RIV year

2009

Released

15.04.2009

Publisher

IEEE Computer Society

Location

Liberec

ISBN

978-1-4244-3339-1

Book

2009 IEEE Symposium on Design and Diagnostics of Electronic Circuits and Systems

Edition

NEUVEDEN

Edition number

NEUVEDEN

Pages from

90

Pages to

95

Pages count

6

URL

Documents

BibTex


@inproceedings{BUT33721,
  author="Tomáš {Martínek} and Matej {Lexa} and Jan {Voženílek}",
  title="Architecture model for approximate palindrome detection",
  annote="Understanding the structure and function of DNA sequences represents an important
area of research in modern biology. One of the interesting structures occurring
in DNA is a palindrome. Biologists believe that palindromes play an important
role in regulation of gene activity and other cell processes because they are
often observed near promoters, introns and specific untranslated regions.
Unfortunately, the time complexity of algorithms for palindrome detection
increases when mutations in the form of character insertions, deletions or
substitutions are taken into consideration. In recent years, several works have
been aimed at acceleration of such algorithms using dedicated circuits capable of
potentially large-scale searching. However, widespread use of such circuits is
often complicated by varying user task details or the need to use a specific
target platform. The objective of this work is therefore to create a model of
hardware architecture for approximate palindrome detection and develop
a technique for automatic mapping of this model to the target platform without
intervention of an experienced designer. The proposed model and the mapping
technique are implemented and evaluated on a family of chips with Virtex5
technology.",
  address="IEEE Computer Society",
  booktitle="2009 IEEE Symposium on Design and Diagnostics of Electronic Circuits and Systems",
  chapter="33721",
  doi="10.1109/DDECS.2009.5012105",
  edition="NEUVEDEN",
  howpublished="online",
  institution="IEEE Computer Society",
  year="2009",
  month="april",
  pages="90--95",
  publisher="IEEE Computer Society",
  type="conference paper"
}