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Testing the order of Markov dependence in DNA sequences

Pardo Llorente, Leandro and Menéndez Calleja, María Luisa and Pardo Llorente, María del Carmen and Zografos, Konstantinos (2011) Testing the order of Markov dependence in DNA sequences. Methodology and computing in applied probability, 13 (1). pp. 59-74. ISSN 1387-5841

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Abstract

DNA or protein sequences are usually modeled as probabilistic phenomena. The simplest model is created on the assumption that the nucleotides at the various sites are independently distributed. Usually the type of nucleotide at some site depends on the type at another site and therefore the DNA sequence is modeled as a Markov chain of random variables taking on the values A, G, C and T corresponding to the four nucleotides. First order or higher order Markov models provide better fit to a DNA sequence. Based on this remark, the aim of this paper is to present and study a family of test statistics for testing order Markov dependence in DNA sequences. This new family includes as a particular case the classical likelihood ratio test. A simulation study is presented in order to find test statistics, in this family, with a better behaviour than the likelihood ratio test.

Item Type:Article
Uncontrolled Keywords:DNA sequence; Markov dependence; Likelihood ratio test; Phi-divergence test statistics; Divergence; Chain
Subjects:Sciences > Mathematics > Applied statistics
ID Code:17330
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Deposited On:05 Dec 2012 09:20
Last Modified:07 Feb 2014 09:45

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