A fast retrieval of DNA sequences using histogram information

Qiu Chen; Koji Kotani; Feifei Lee; Tadahiro Ohmi

doi:10.1109/FITME.2009.137

A fast retrieval of DNA sequences using histogram information

Qiu Chen, Koji Kotani, Feifei Lee, Tadahiro Ohmi

ENG - Electronic Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English
Title of host publication	2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009
Pages	529-532
Number of pages	4
DOIs	https://doi.org/10.1109/FITME.2009.137
Publication status	Published - 2009 Dec 1
Event	2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009 - Sanya, China Duration: 2009 Dec 13 → 2009 Dec 14

Publication series

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

Other

Other	2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009
Country	China
City	Sanya
Period	09/12/13 → 09/12/14

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

Access to Document

10.1109/FITME.2009.137

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Chen, Q., Kotani, K., Lee, F., & Ohmi, T. (2009). A fast retrieval of DNA sequences using histogram information. In 2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009 (pp. 529-532). [5381043] (2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009). https://doi.org/10.1109/FITME.2009.137

A fast retrieval of DNA sequences using histogram information. / Chen, Qiu; Kotani, Koji; Lee, Feifei; Ohmi, Tadahiro.

2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009. 2009. p. 529-532 5381043 (2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Chen, Q, Kotani, K, Lee, F & Ohmi, T 2009, A fast retrieval of DNA sequences using histogram information. in 2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009., 5381043, 2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009, pp. 529-532, 2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009, Sanya, China, 09/12/13. https://doi.org/10.1109/FITME.2009.137

Chen Q, Kotani K, Lee F, Ohmi T. A fast retrieval of DNA sequences using histogram information. In 2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009. 2009. p. 529-532. 5381043. (2009 2nd International Conference on Future Information Technology and Management Engineering, FITME 2009). https://doi.org/10.1109/FITME.2009.137

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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.",

keywords = "DNA sequence, Fast retrieval, Histogram information, Smith-Waterman algorithm",

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AB - 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.

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