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Distinguish Coding And Noncoding Sequences In A Complete Genome Using Fourier Transform

Zhou, Yu , Zhou, Li-Qian , Yu, Zu-Guo, & Anh, Vo V. (2007) Distinguish Coding And Noncoding Sequences In A Complete Genome Using Fourier Transform. In Third International Conference on Natural Computation (ICNC 2007), 24-27 August 2007, Haikou, China.

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Abstract

A Fourier transform method is proposed to distinguish coding and non-coding sequences in a complete genome based on a number sequence representation of the DNA sequence proposed in our previous paper (Zhou et al., J. Theor. Biol. 2005) and the imperfect periodicity of 3 in protein coding sequences. The three parameters P_x(S) (1), P_x(S) (1/3) and P_x(S) (1/36) in the Fourier transform of the number sequence representation of DNA sequences are selected to form a three-dimensional parameter space. Each DNA sequence is then represented by a point in this space. The points corresponding to coding and non-coding sequences in the complete genome of prokaryotes are seen to be divided into different regions. If the point (P_x(�ar S) (1), Px(�ar S) (1/3), P_x(�ar S) (1/36)) for a DNA sequence is situated in the region corresponding to coding sequences, the sequence is distinguished as a coding sequence; otherwise, the sequence is classified as a noncoding one. Fisher's discriminant algorithm is used to study the discriminant accuracy. The average discriminant accuracies pc, pnc, qc and qnc of all 51 prokaryotes obtained by the present method reach 81.02%, 92.27%, 80.77% and 92.24% respectively.

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ID Code: 14326
Item Type: Conference Paper
Keywords: Fourier transforms, biocomputing
DOI: 10.1109/ICNC.2007.333
ISBN: 9780769528755
Subjects: Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > APPLIED MATHEMATICS (010200) > Biological Mathematics (010202)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400) > Genetics not elsewhere classified (060499)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2007 IEEE
Copyright Statement: Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.
Deposited On: 07 Aug 2008
Last Modified: 29 Feb 2012 23:40

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