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Local matching of random restriction maps

Part of: Combinatorial probability Limit theorems

Published online by Cambridge University Press:  14 July 2016

Mengxiang Tang  and
Michael S. Waterman
Mengxiang Tang*
Affiliation:
University of Southern California
Michael S. Waterman*
Affiliation:
University of Southern California
*
∗ Postal address: Mathematics Department, University of Southern California, Los Angeles, CA 90089-1113, USA.
∗ Postal address: Mathematics Department, University of Southern California, Los Angeles, CA 90089-1113, USA.
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Abstract

Optical mapping is a new technique to generate restriction maps of DNA easily and quickly. DNA restriction maps can be aligned by comparing corresponding restriction fragment lengths. To relate, organize, and analyse these maps it is necessary to rapidly compare maps. The issue of the statistical significance of approximately matching maps then becomes central, as in BLAST with sequence scoring. In this paper, we study the approximation to the distribution of counts of matched regions of specified length when comparing two DNA restriction maps. Distributional results are given to enable us to compute p-values and hence to determine whether or not the two restriction maps are related. The key tool used is the Chen-Stein method of Poisson approximation. Certain open problems are described.

Keywords

Restriction mapsmatchingChen-Stein method

MSC classification

Primary: 60C05: Combinatorial probability
Secondary: 60F20: Zero-one laws
Type
Research Papers
Information
Journal of Applied Probability , Volume 38 , Issue 2 , June 2001 , pp. 335 - 356
Copyright
Copyright © Applied Probability Trust 2001 

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