Alignment-free genome sequence comparison method based on pair transition difference of k-words

This paper proposes a novel alignment-free genome sequence comparison method using pair transition property of k-words. In the proposed method, difference between pair transition of k-words is extracted from genome sequence as feature vector. Using the statistical distances metric and the phylogenetic tree, the classification performance of proposed method is identified. Also, to reduce the computational complexity, the selection method of pair word is introduced. Finally, the performance of proposed method is compared with conventional alignment-free methods for 54 MT genomes with respect to the RF distance and the computational complexity.