Statistical analysis of gene and intergenic DNA sequences

D. Kugiumtzis and A. Provata

Physica A: Statistical Mechanics and its Applications, 2004, vol. 342, issue 3, 623-638

Abstract: Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate specifically on genes and intergenic regions. To estimate the level and type of correlation in these regions we apply various statistical methods inspired from nonlinear time series analysis, namely the probability distribution of tuplets, the Mutual Information and the Identical Neighbour Fit. The methods are suitably modified to work on symbolic sequences and they are first tested for validity on sequences obtained from well-known simple deterministic and stochastic models. Then they are applied to the DNA sequence of chromosome 1 of arabidopsis thaliana. The results suggest that correlations do exist in the DNA sequence but they are weak and that intergenic sequences tend to be more correlated than gene sequences. The use of statistical tests with surrogate data establish these findings in a rigorous statistical manner.

Keywords: Long-range correlations; DNA sequence; Genes; Intergenic regions; Nonlinear analysis of time series; Surrogate data test (search for similar items in EconPapers)
Date: 2004
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Citations: View citations in EconPapers (2)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:342:y:2004:i:3:p:623-638

DOI: 10.1016/j.physa.2004.05.070

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