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Comparaison de séquences répétées en tandem et application à la génétique

Sèverine Bérard 1
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Tandem repeats consists of a heterogeneous tandem array of a repeat unit. Microsatellites and minisatellites belong to this class of genetic sequences. In this thesis, we deal with the problem of alignment of tandem repeats under a specific evolutionary model. This model, termed sse, involves 5 operations : mutation, insertion and deletion (the classical operations in string alignment) plus tandem amplification and tandem contraction. An amplification duplicates a character to produce
an identical character next to it. Contraction removes a character if and only if it is next to an identical character. The amplification (resp. contraction) is said "of arity n and order m" if it copies (resp. deletes) m motifs n times. We propose an algorithm to compute the distance between two tandem repeats under the SSe model where amplifications and contractions are of arity 1 and order 1. This problem is difficult because of the non-commutativity of operations. We have integrated our algorithm in a software named MS Align. It is the first software to align minisatellites maps. We have study biological data from human minisatellite MSY1. Our evolutionary model well fit this kind of DNA sequences. We have construct phylogenetic trees similar to those constructed with other markers on Y chromosome. We observed that our tree shows a better resolution. A part of this thesis is devoted to the general problem obtained when relaxing the constraints on amplifications and contractions.
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Submitted on : Monday, April 19, 2004 - 6:19:16 PM
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Sèverine Bérard. Comparaison de séquences répétées en tandem et application à la génétique. Autre [cs.OH]. Université Montpellier II - Sciences et Techniques du Languedoc, 2003. Français. ⟨tel-00005930⟩

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