An improved fast search method using histogram features for DNA sequence database

Qiu Chen, Feifei Lee, Koji Kotani, Tadahiro Ohmi

Research output: Contribution to journalArticlepeer-review

Abstract

In this paper, we propose an efficient hierarchical DNA sequence search method to improve the search speed while the accuracy is being kept constant. For a given query DNA sequence, firstly, a fast local search method using histogram features is used as a filtering mechanism before scanning the sequences in the database. An overlapping processing is newly added to improve the robustness of the algorithm. 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 more efficient for DNA sequence search.

Original languageEnglish
Pages (from-to)569-572
Number of pages4
JournalWorld Academy of Science, Engineering and Technology
Volume70
Publication statusPublished - 2010 Sep 1

Keywords

  • DNA sequence
  • Fast search
  • Histogram feature
  • Local search
  • Smith-Waterman algorithm

ASJC Scopus subject areas

  • Engineering(all)

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