Numerical characterization of DNA sequences based on the  k ‐step Markov chain transition probability | Zendy

Dai Qi | Zendy; Liu XiaoQing | Zendy; Wang TianMing | Zendy

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Numerical characterization of DNA sequences based on the k ‐step Markov chain transition probability

Author(s) -

Dai Qi,

Liu XiaoQing,

Wang TianMing

Publication year - 2006

Publication title -

journal of computational chemistry

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.907

H-Index - 188

eISSN - 1096-987X

pISSN - 0192-8651

DOI - 10.1002/jcc.20471

Subject(s) - markov chain , transition (genetics) , mathematics , series (stratigraphy) , sequence (biology) , dna , chain (unit) , characterization (materials science) , combinatorics , invariant (physics) , additive markov chain , discrete mathematics , markov model , variable order markov model , genetics , physics , biology , statistics , gene , astronomy , mathematical physics , optics , paleontology

A DNA sequence can be regarded as a discrete‐time Markov chain. Based on k ‐step transition probabilities, we construct a series of 4 × 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. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006

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