A local search method using histogram features for fast retrieval of DNA sequences

Qiu Chen, Koji Kotani, Feifei Lee, Tadahiro Ohmi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

DNA sequence retrieval is a very important topic in bioinformatics algorithm development. However, this task usually spends much computational time to search on large DNA sequence database. In this paper, an efficient hierarchical method is proposed to improve the search speed while the accuracy is being kept constant. For a given query sequence, firstly, a fast local search method using histogram features is used as a filtering mechanism before scanning the sequences in the database. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith-Waterman algorithm is then applied to each remainder sequences. Experimental results using GenBank sequence data show the proposed method combining histogram information and Smith-Waterman algorithm is a more efficient algorithm for DNA sequence retrieval.

Original languageEnglish
Title of host publicationWCE 2010 - World Congress on Engineering 2010
Pages395-398
Number of pages4
Publication statusPublished - 2010 Dec 1
EventWorld Congress on Engineering 2010, WCE 2010 - London, United Kingdom
Duration: 2010 Jun 302010 Jul 2

Publication series

NameWCE 2010 - World Congress on Engineering 2010
Volume1

Other

OtherWorld Congress on Engineering 2010, WCE 2010
CountryUnited Kingdom
CityLondon
Period10/6/3010/7/2

Keywords

  • DNA sequence
  • Fast retrieval
  • Histogram information
  • Local search
  • Smith-Waterman algorithm

ASJC Scopus subject areas

  • Computer Science(all)
  • Engineering(all)

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