Approximate word matches between two random sequences
Conrad J. Burden, Miriam R. Kantorovitz, and Susan R. Wilson
Source: Ann. Appl. Probab. Volume 18, Number 1 (2008), 1-21.
Abstract
Given two sequences over a finite alphabet , the D2 statistic is the number of m-letter word matches between the two sequences. This statistic is used in bioinformatics for expressed sequence tag database searches. Here we study a generalization of the D2 statistic in the context of DNA sequences, under the assumption of strand symmetric Bernoulli text. For k<m, we look at the count of m-letter word matches with up to k mismatches. For this statistic, we compute the expectation, give upper and lower bounds for the variance and prove its distribution is asymptotically normal.
Primary Subjects: 60F17, 92D20
Keywords: DNA sequences; sequence comparison; word matches
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Links and Identifiers
Permanent link to this document: http://projecteuclid.org/euclid.aoap/1199890013
Digital Object Identifier: doi:10.1214/07-AAP452
Mathematical Reviews number (MathSciNet):
MR2380889
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