Open Access

Comparative Genomics via Wavelet Analysis for Closely Related Bacteria

EURASIP Journal on Advances in Signal Processing20042004:890421

DOI: 10.1155/S1110865704309170

Received: 26 February 2003

Published: 21 January 2004

Abstract

Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavelet analysis to perform comparative genomics. First, global comparison using wavelet analysis gives the difference at a quantitative level. Then local comparison using keto-excess or purine-excess plots shows precise positions of inversions, translocations, and horizontally transferred DNA fragments. We firstly found that the level of energy spectra difference is related to the similarity of bacteria strains; it could be a quantitative index to describe the similarities of genomes. The strategy is described in detail by comparisons of closely related strains: S.typhi CT18, S.typhi Ty2, S.typhimurium LT2, H.pylori 26695, and H.pylori J99.

Keywords

comparative genomics gene discovery wavelet analysis bacterial genome

Authors’ Affiliations

(1)
Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary

Copyright

© Song et al. 2004