Comparing bacterial genomes from linear orders of patterns

Authors:
Frédéric Guyon;Alain Guénoche
Affiliations:
INSERM U726, Université Paris 7, 2 place Jussieu, 75005 Paris, France and IML-CNRS, 163 Av. de Luminy, 13009 Marseille, France;INSERM U726, Université Paris 7, 2 place Jussieu, 75005 Paris, France and IML-CNRS, 163 Av. de Luminy, 13009 Marseille, France
Venue:
Discrete Applied Mathematics
Year:
2008

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Abstract

We compare complete genomes from common words denoted MUMs for maximum unique matches. They allow to transform each genome into a linear order. We first evaluate the minimum length of a MUM shared by two genomes to be significant. Secondly, we compute maximal common chains of elements, that are in the same order in genomes. From these chains we define conserved genome segments as long DNA fragments having MUMs in the same order and with a bounded gap length between them. The resulting small number of segments allow to detect main evolutionary events as reversal or transposition of these fragments.