A discrete autoregressive process as a model for short-range correlations in DNA sequences

M. Dehnert, W.E. Helm and M.-Th. Hütt

Physica A: Statistical Mechanics and its Applications, 2003, vol. 327, issue 3, 535-553

Abstract: We present a direct way to model short- and medium-range correlations in DNA sequences and to separate them from long-range correlations. To do so, we discuss symbol sequences generated by a discrete autoregressive process of order p, DAR(p). These sequences display higher-order Markov properties but are based on very few parameters. The aim of our investigation is (1) to introduce with such DAR(p) processes a parameter-efficient tool for generating higher-order Markov processes on a discrete alphabet, (2) to study, how the parameters of the process determine the statistical properties of the sequence and (3) to provide the mathematical tools for estimating the parameters from a given experimental sequence. The statistical properties of the generated sequences, expressed in terms of parameters in the DAR(p) process, are monitored with methods from information theory. The implications of our findings for DNA sequences are discussed and some application is given. In particular, it is shown, how short-range correlations in DNA sequences can be parameterised by such a process.

Keywords: Long-range correlation; DNA analysis; Entropy; Mutual information; Markov process of higher order; Discrete autoregressive process (search for similar items in EconPapers)
Date: 2003
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (4)

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S0378437103003996
Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:327:y:2003:i:3:p:535-553

DOI: 10.1016/S0378-4371(03)00399-6

Access Statistics for this article

Physica A: Statistical Mechanics and its Applications is currently edited by K. A. Dawson, J. O. Indekeu, H.E. Stanley and C. Tsallis

More articles in Physica A: Statistical Mechanics and its Applications from Elsevier
Bibliographic data for series maintained by Catherine Liu ().