A Novel Real-Time Genome Comparison Method Using Discrete Wavelet Transform

Keywords

alignment-free; clustering; DWT; phylogenetic analysis

Abstract

Real-time genome comparison is important for identifying unknown species and clustering organisms. We propose a novel method that can represent genome sequences of different lengths as a 12-dimensional numerical vector in real time for this purpose. Given a genome sequence, a binary indicator sequence of each nucleotide base location is computed, and then discrete wavelet transform is applied to these four binary indicator sequences to attain the respective power spectra. Afterward, moments of the power spectra are calculated. Consequently, the 12-dimensional numerical vectors are constructed from the first three order moments. Our experimental results on various data sets show that the proposed method is efficient and effective to cluster genes and genomes. It runs significantly faster than other alignment-free and alignment-based methods.

Publication Date

4-1-2018

Publication Title

Journal of Computational Biology

Volume

25

Issue

4

Number of Pages

405-416

Document Type

Article

Personal Identifier

scopus

DOI Link

https://doi.org/10.1089/cmb.2017.0115

Socpus ID

85045203188 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/85045203188

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