title: A novel method for comparative analysis of DNA sequences by Ramanujan-Fourier transform.
abstract: Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on high level of sequence identity. However, most of the existing alignment-free methods do not employ true full information content of sequences and thus can not accurately reveal similarities and differences among DNA sequences. We present a novel alignment-free computational method for sequence analysis based on Ramanujan-Fourier transform (RFT), in which complete information of DNA sequences is retained. We represent DNA sequences as four binary indicator sequences and apply RFT on the indicator sequences to convert them into frequency domain. The Euclidean distance of the complete RFT coefficients of DNA sequences are used as similarity measures. To address the different lengths of RFT coefficients in Euclidean space, we pad zeros to short DNA binary sequences so that the binary sequences equal the longest length in the comparison sequence data. Thus, the DNA sequences are compared in the same dimensional frequency space without information loss. We demonstrate the usefulness of the proposed method by presenting experimental results on hierarchical clustering of genes and genomes. The proposed method opens a new channel to biological sequence analysis, classification, and structural module identification.
authors.affiliation: 1 College of Information Systems and Technology, University of Phoenix , Chicago, Illinois.
authors.forename: Changchuan
authors.initials: C
authors.lastname: Yin
authors.forename: Xuemeng E
authors.initials: XE
authors.lastname: Yin
authors.forename: Jiasong
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics*; D005583:Fourier Analysis; D016678:Genome; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004247:DNA
keywords: DNA sequence; Ramanujan-Fourier transform; cluster analysis; phylogenetic trees; similarity measure