title: Alignment-free comparison of genome sequences by a new numerical characterization.
abstract: In order to compare different genome sequences, an alignment-free method has proposed. First, we presented a new graphical representation of DNA sequences without degeneracy, which is conducive to intuitive comparison of sequences. Then, a new numerical characterization based on the representation was introduced to quantitatively depict the intrinsic nature of genome sequences, and considered as a 10-dimensional vector in the mathematical space. Alignment-free comparison of sequences was performed by computing the distances between vectors of the corresponding numerical characterizations, which define the evolutionary relationship. Two data sets of DNA sequences were constructed to assess the performance on sequence comparison. The results illustrate well validity of the method. The new numerical characterization provides a powerful tool for genome comparison.
authors.affiliation: Department of Mathematics, Shaoyang University, Shaoyang, Hunan, China. guohuahhn@163.com
authors.forename: Guohua
authors.initials: G
authors.lastname: Huang
authors.forename: Houqing
authors.initials: H
authors.lastname: Zhou
authors.forename: Yongfan
authors.initials: Y
authors.lastname: Li
authors.forename: Lixin
authors.initials: L
authors.lastname: Xu
mesh_terms: D000818:Animals; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D016678:Genome / Q000235:genetics*; D006801:Humans; D008322:Mammals / Q000235:genetics; D009154:Mutation / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D009716:Numerical Analysis, Computer-Assisted; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D009711:Nucleotides