A hybrid technique for the periodicity characterization of genomic sequence data

Authors:
Julien Epps
Affiliations:
School of Electrical Engineering and Telecommunications, The University of New South Wales, Sydney, NSW, Australia and National Information Communication Technology Australia, Australian Technolog ...
Venue:
EURASIP Journal on Bioinformatics and Systems Biology - Special issue on applications of signal procesing techniques to bioinformatics, genomics, and proteomics
Year:
2009

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Abstract

Many studies of biological sequence data have examined sequence structure in terms of periodicity, and various methods for measuring periodicity have been suggested for this purpose. This paper compares two such methods, autocorrelation and the Fourier transform, using synthetic periodic sequences, and explains the differences in periodicity estimates produced by each. A hybrid autocorrelation--integer period discrete Fourier transform is proposed that combines the advantages of both techniques. Collectively, this representation and a recently proposed variant on the discrete Fourier transform offer alternatives to the widely used autocorrelation for the periodicity characterization of sequence data. Finally, these methods are compared for various tetramers of interest in C. elegans chromosome I.