Computing the likelihood of sequence segmentation under Markov modelling

Laurent Guéguen (1)

1 BPGE - Bioinformatique, phylogénie et génomique évolutive

I tackle the problem of partitioning a sequence into homogeneous segments, where homogeneity is defined by a set of Markov models. The problem is to study the likelihood that a sequence is divided into a given number of segments. Here, the moments of this likelihood are computed through an efficient algorithm. Unlike methods involving Hidden Markov Models, this algorithm does not require probability transitions between the models. Among many possible usages of the likelihood, I present a maximum \textit{a posteriori} probability criterion to predict the number of homogeneous segments into which a sequence can be divided, and an application of this method to find CpG islands.

Mots clés: sequence analysis; Markov model; segmentation; homogeneity

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Laurent Guéguen. Computing the likelihood of sequence segmentation under Markov modelling. 2009. ⟨hal-00432383⟩