Gene comparison based on the repetition of single-nucleotide structure patterns.
According to the repetition structure patterns of single-nucleotides, we propose a novel digital representation method to characterize primary DNA sequences. Based on this representation we give a new RP-SP (repeat and space) vector to compute the distance of different sequences. The examination of similarities/dissimilarities among different sequences illustrates the utility of the proposed RP-SP vector distance. Then, we use the proposed RP-SP vector method to analyze two groups of genomes, 15 E. coli genomes and 31 mitochondrial genomes. For comparison, we also apply other alignment-free methods to the two groups of genomes. The results show that the proposed method can distinguish characteristics of different genomes and used to reconstruct the phylogenetic tree of different genomes.
College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, Hebei 050043, People's Republic of China. zhqi_yh2004@yahoo.com.cn
Zhao-Hui
ZH
Qi
Ming-Hui
MH
Du
Xiao-Qin
XQ
Qi
Li-Juan
LJ
Zheng
D000818:Animals; D001483:Base Sequence; D030541:Databases, Genetic; D016680:Genome, Bacterial; D054629:Genome, Mitochondrial; D023281:Genomics / Q000379:methods*; D006801:Humans; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*