Numerical characterization of DNA sequences based on the k-step Markov chain transition probability.
A DNA sequence can be regarded as a discrete-time Markov chain. Based on k-step transition probabilities, we construct a series of 4 x 4 k-step transition matrices to characterize the DNA primary sequences. According to the properties of Markov chains, we obtain distributions of A, T, C and G, and analyze the changes among them from yesterday to tomorrow. We can calculate the probabilities of nucleotide triples of DNA primary sequences. Finally, we introduce a correlation of this kind of transition matrices and consider it as an invariant to analyze the similarities/dissimilarities of DNA sequences.
Dai
Qi
Q
Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, People's Republic of China. daiailiu2004@yahoo.com.cn
Liu
Xiao-Qing
XQ
Wang
Tian-Ming
TM
D000241:Adenosine / Q000737:chemistry; D000818:Animals; D003562:Cytidine / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D019143:Evolution, Molecular; D006151:Guanosine / Q000737:chemistry; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D013936:Thymidine / Q000737:chemistry
D006151:Guanosine; D003562:Cytidine; D004247:DNA; D000241:Adenosine; D013936:Thymidine