Multi-scale parametric spectral analysis for exon detection in DNA sequences based on forward-backward linear prediction and singular value decomposition of the double-base curves

Miew Keen Choong, Hong Yan

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Abstract

This paper presents a new method for exon detection in DNA sequences based on multi-scale parametric spectral analysis. A forward-backward linear prediction (FBLP) with the singular value decomposition (SVD) algorithm FBLP-SVD is applied to the double-base curves (DB-curves) of a DNA sequence using a variable moving window sizes to estimate the signal spectrum at multiple scales. Simulations are done on short human genes in the range of 11bp to 2032bp and the results show that our proposed method out-performs the classical Fourier transform method. The multi-scale approach is shown to be more effective than using a single scale with a fixed window size. In addition, our method is flexible as it requires no training data.

Original languageEnglish
Pages (from-to)273-8
Number of pages6
JournalBioinformation
Volume2
Issue number7
Publication statusPublished - 12 Feb 2008
Externally publishedYes

Bibliographical note

Copyright the Author(s) 2008. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • Journal Article

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