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Detecting a changed segment in DNA sequences

Lookup NU author(s): Dr Peter Avery, Dr Daniel Henderson


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Non-coding deoxyribonucleic acid (DNA) can typically be modelled by a sequence of Bernoulli random variables by coding one base, e.g. T, as 1 and other bases as 0. If a segment of a sequence is functionally important, the probability of a 1 will be different in this changed segment from that in the surrounding DNA. It is important to be able to see whether such a segment occurs in a particular DNA sequence and to pin-point it so that a molecular biologist can investigate its possible function. Here we discuss methods for testing the occurrence of such a changed segment and how to estimate the end points of it. Maximum-likelihood-based methods are not very tractable and so a nonparametric method based on the approach of Pettitt has been developed. The problem and its solution are illustrated by a specific DNA example.

Publication metadata

Author(s): Avery PJ; Henderson DA

Publication type: Article

Publication status: Published

Journal: Journal of the Royal Statistical Society. Series C: Applied Statistics

Year: 1999

Volume: 48

Issue: 4

Pages: 489-503

Print publication date: 01/01/1999

ISSN (print): 0035-9254

ISSN (electronic): 1467-9876

Publisher: Wiley-Blackwell Publishing Ltd.


DOI: 10.1111/1467-9876.00167


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