Detecting a changed segment in DNA sequences

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Abstract:

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.

Keywords: Bernoulli sequence; Changepoints; DNA sequence analysis; Kolmogorov–Smirnov statistics; Nonparametric methods

Document Type: Original Article

DOI: http://dx.doi.org/10.1111/1467-9876.00167

Affiliations: University of Newcastle, UK

Publication date: January 1, 1999

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