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

Journal of computational biology: A journal of computational molecular cell biology

Senthil B.Girimurugan^2¹  Hsin-HsiungHuang^1² 

[1] Department of Mathematics, Florida Gulf Coast University, Fort Myers, Florida^2;Department of Statistics, University of Central Florida, Orlando, Florida^1

关键词: alignment-free;    clustering;    DWT;    phylogenetic analysis;   

DOI  :  10.1089/cmb.2017.0115

学科分类：生物科学（综合）

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

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.

【 授权许可】

Unknown