Research on DNA Sequence Homology Based on Second Order Markov Model

Abstract

DNA sequence homology is a critical and fundamental problem in bioinformatics. In this paper, we solve this problem by use of the second order Markov modal instead of traditional sequence alignment because DNA character sequence meets the Markov properties. Hence, the characteristics of DNA sequences are represented by using their two-step transition probabilities matrices. The similarity degree measurement between two different DNA sequences is defined. Our DSHM algorithm is put forward which is implemented by MyEclipse. The contrast experiments are done between DSHM and other two methods. The experimental results show that DSHM algorithm can determine DNA sequence homology correctly in the more effective way.