A fast retrieval of DNA sequences using histogram information

Qiu Chen, Koji Kotani, Feifei Lee, Tadahiro Ohmi

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

2 Citations (Scopus)

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. This paper presents an efficient hierarchical method to improve the search speed while the accurate is being kept constant. For a given query sequence, firstly, a fast histogram method is used to scan 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 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 publication2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009
Pages529-532
Number of pages4
DOIs
Publication statusPublished - 2009 Dec 1
Event2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009 - Sanya, China
Duration: 2009 Dec 132009 Dec 14

Publication series

Name2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009

Other

Other2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009
CountryChina
CitySanya
Period09/12/1309/12/14

Keywords

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

ASJC Scopus subject areas

  • Management of Technology and Innovation
  • Information Systems
  • Information Systems and Management

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