A MARKOV ANALYSIS OF DNA-SEQUENCES
A MARKOV ANALYSIS OF DNA-SEQUENCES
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DOI：
10.1016/0022-5193(83)90251-5
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发表时间：
1983-01-01
影响因子：
2
通讯作者：
ALMAGOR, H
中科院分区：
文献类型：
--
作者：
ALMAGOR, H
A model is presented to study the DNA sequence as a Markov process. Some basic biological or chemical features of nucleic acids may stand behind the frequencies of dinucleotides (doublets) in these chains. Comparing patterns of doublet frequencies in DNA of different organisms was shown to be a fruitful approach to some phylogenetic questions. Grantham formulated mRNA sequence indices, some of which involve certain doublet frequencies. He suggested that using these indices may provide indications of the molecular constraints existing during gene evolution. Nussinov has shown that a set of dinucleotide preference rules holds consistently for eukaryotes, and suggested a strong correlation between these rules and degenerate codon usage. Gruenbaum, Cedar and Razin found that methylation in eukaryotic DNA occurs exclusively at C-G sites. Important biological information thus seems to be contained in the doublet frequencies. One of the basic questions to be asked (the correlation question) is to what extent are the 64 trinucleotide (triplet) frequencies measured in a sequence determined by the 16 doublet frequencies in the same sequence. The DNA is described here as a Markov process, with the nucleotides being outcomes of a sequence generator. Answering the correlation question mentioned above means finding the order of the Markov process. The difficulty is that natural sequences are of finite length, and statistical noise is quite strong. Even for a 16,000 nucleotide long sequence (like that of the human mitochondrial genome) the finite length effect cannot be neglected. Using the Markov chain model, the correlation between doublet and triplet frequencies can, however, be determined even for finite sequences, taking proper account for the finite length. Two natural DNA sequences, the human mitochondrial genome and the SV40 DNA, are analyzed as examples of the method.
