Moderate deviations for word counts in biological sequences

Moderate deviations for word counts in biological sequences

Sarah Behrens and Matthias Löwe

Source: J. Appl. Probab. Volume 46, Number 4 (2009), 1020-1037.

Abstract

We derive a moderate deviation principle for word counts (which is extended to counts of multiple patterns) in biological sequences under different models: independent and identically distributed letters, homogeneous Markov chains of order 1 and $m$, and, in view of the codon structure of DNA sequences, Markov chains with three different transition matrices. This enables us to approximate P-values for the number of word occurrences in DNA and protein sequences in a new manner.

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Primary Subjects: 60F99, 92D20

Secondary Subjects: 60J10, 60J20, 60G50

Keywords: Moderate deviations; Markov chain; word counts; motifs; biological sequence analysis

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Links and Identifiers

Permanent link to this document: http://projecteuclid.org/euclid.jap/1261670686
Digital Object Identifier: doi:10.1239/jap/1261670686
Zentralblatt MATH identifier: 05665453
Mathematical Reviews number (MathSciNet): MR2582704

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