Similarity searching in DNA sequences by spectral distortion measures

Pham, Tuan D. (2006) Similarity searching in DNA sequences by spectral distortion measures. In: Proceedings of the 6th Industrial Conference on Data Mining (4065), pp. 24-37. From: ICDM 2006 6th Industrial Conference on Data Mining, 14-15 July 2006, Leipzig, Germany.

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Abstract

Searching for similarity among biological sequences is an important research area of bioinformatics because it can provide insight into the evolutionary and genetic relationships between species that open doors to new scientific discoveries such as drug design and treament. In this paper, we introduce a novel measure of similarity between two biological sequences without the need of alignment. The method is based on the concept of spectral distortion measures developed for signal processing. The proposed method was tested using a set of six DNA sequences taken from Escherichia coli K-12 and Shigella flexneri, and one random sequence. It was further tested with a complex dataset of 40 DNA sequences taken from the GenBank sequence database. The results obtained from the proposed method are found superior to some existing methods for similarity measure of DNA sequences.

Item ID: 4342
Item Type: Conference Item (Refereed Research Paper - E1)
Keywords: DNA; similarity measure
ISBN: 978-3-540-36036-0
ISSN: 1611-3349
Projects and Grants: Industrial Conference on Data Mining ICDM
Date Deposited: 19 Nov 2009 05:36
SEO Codes: 92 HEALTH > 9202 Health and Support Services > 920203 Diagnostic Methods @ 34%
92 HEALTH > 9204 Public Health (excl. Specific Population Health) > 920412 Preventive Medicine @ 33%
92 HEALTH > 9201 Clinical Health (Organs, Diseases and Abnormal Conditions) > 920102 Cancer and Related Disorders @ 33%
Citation Count from Web of Science Web of Science 1
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