The Distribution of Short Word Match Counts between Markovian Sequences

Conrad J. Burden; Paul Leopardi; Sylvain Forêt

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Paper

The Distribution of Short Word Match Counts between Markovian Sequences

Topics: Biostatistics and Stochastic Models; Pattern Recognition, Clustering and Classification; Sequence Analysis

In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, 25-33, 2013 , Barcelona, Spain

Authors: Conrad J. Burden ; Paul Leopardi and Sylvain Forêt

Affiliation: Australian National University, Australia

ISBN: 978-989-8565-35-8

ISSN: 2184-4305

Keyword(s): Word Matches, Biological Sequence Comparison.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Biostatistics and Stochastic Models ; Pattern Recognition, Clustering and Classification ; Sequence Analysis

Abstract: The D2 statistic, which counts the number of word matches between two given sequences, has long been proposed as a measure of similarity for biological sequences. Much of the mathematically rigorous work carried out to date on the properties of the D2 statistic has been restricted to the case of ‘Bernoulli’ sequences composed of identically and independently distributed letters. Here the properties of the distribution of this statistic for the biologically more realistic case of Markovian sequences is studied. The approach is novel in that Markovian dependency is defined for sequences with periodic boundary conditions, and this enables exact analytic formulae for the mean and variance to be derived. The formulae are confirmed using numerical simulations, and asymptotic approximations to the full distribution are tested.

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Paper citation in several formats:

J. Burden, C.; Leopardi, P. and Forêt, S. (2013). The Distribution of Short Word Match Counts between Markovian Sequences.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 25-33. DOI: 10.5220/0004203700250033

@conference{bioinformatics13,
author={Conrad {J. Burden}. and Paul Leopardi. and Sylvain Forêt.},
title={The Distribution of Short Word Match Counts between Markovian Sequences},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={25-33},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004203700250033},
isbn={978-989-8565-35-8},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - The Distribution of Short Word Match Counts between Markovian Sequences
SN - 978-989-8565-35-8
AU - J. Burden, C.
AU - Leopardi, P.
AU - Forêt, S.
PY - 2013
SP - 25
EP - 33
DO - 10.5220/0004203700250033