Title

On relationship of Z-curve and Fourier approaches for DNA coding sequence classification

Authors

Ngai-Fong Law*; Kin-On Cheng and Wan-Chi Siu

Affiliation

Centre for Multimedia Signal Processing, Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong

Email

ennflaw@polyu.edu.hk; *Corresponding author

Phone

+852-2766 4746

Fax

+852-2362 8439

Article Type

Prediction Model

Date

received October 20, 2006; accepted November 02, 2006; published online November 14, 2006
 

Abstract

Z-curve features are one of the popular features used in exon/intron classification. We showed that although both Z-curve and Fourier approaches are based on detecting 3-periodicity in coding regions, there are significant differences in their spectral formulation. From the spectral formulation of the Z-curve, we obtained three modified sequences that characterize different biological properties.  Spectral analysis on the modified sequences showed a much more prominent 3-periodicity peak in coding regions than the Fourier approach.  For long sequences, prominent peaks at 2P/3 are observed at coding regions, whereas for short sequences, clearly discernible peaks are still visible.  Better classification can be obtained using spectral features derived from the modified sequences.

Keywords

Z-Curve approach; FT analysis; DNA Sequence; coding region; spectral analysis
 

Citation

Law et al., Bioinformation 1(7): 242-246 (2006)
 

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.