Title: Detection and 2-Dimensional display of short tandem repeats based on signal decomposition

Authors: Rong Jiang; Hong Yan

Addresses: School of Electrical and Information Engineering, University of Sydney, NSW 2006, Australia. ' Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong

Abstract: This paper presents a wavelet-based Empirical Mode Decomposition (EMD) to detect short tandem repeats in DNA sequences. A wavelet subspace algorithm combined with EMD is introduced as a pre-processor and a Cross-Correlation Analysis (CCA) is applied as a post-processor to create subspaced Intrinsic Mode Functions (IMFs). The new proposed method is called the Empirical Mode and Wavelet Decomposition (EMWD). The algorithms can display the power spectral density in the two-dimensional frequency-time (f-t) plane efficiently for both very long signals and short signals. Simulations are applied on the real human DNA sequences from public data source Genbank (http://www.ncbi.nlm.nih.gov/Genbank/). Application of the EMWD algorithms to the short tandem repeat detection has achieved an averaged accuracy of 98.5%.

Keywords: short tandem repeats; gene analysis; Hilbert Huang transform; wavelets; nucleotides; EMWD; empirical mode decomposition; wavelet decomposition; bioinformatics; DNA sequences; signal decomposition.

DOI: 10.1504/IJDMB.2011.045416

International Journal of Data Mining and Bioinformatics, 2011 Vol.5 No.6, pp.661 - 690

Received: 10 May 2009
Accepted: 07 May 2010
Published online: 24 Jan 2015 *

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