title: Alignment free comparison: similarity distribution between the DNA primary sequences based on the shortest absent word.
abstract: This work proposes an alignment free comparison model for the DNA primary sequences. In this paper, we treat the double strands of the DNA rather than single strand. We define the shortest absent word of the double strands between the DNA sequences and some properties are studied to speed up the algorithm for searching the shortest absent word. We present a novel model for comparison, in which the similarity distribution is introduced to describe the similarity between the sequences. A distance measure is deduced based on the Shannon entropy meanwhile is used in phylogenetic analysis. Some experiments show that our model performs well in the field of sequence analysis.
authors.affiliation: College of Sciences, Northeastern University, Shenyang, China.
authors.forename: Lianping
authors.initials: L
authors.lastname: Yang
authors.forename: Xiangde
authors.initials: X
authors.lastname: Zhang
authors.forename: Hegui
authors.initials: H
authors.lastname: Zhu
mesh_terms: D000465:Algorithms; D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D019277:Entropy; D006801:Humans; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D004272:DNA, Mitochondrial