A general method for common intervals

Abstract: Given an elementary chain of vertex set V, seen as a labelling of V by the set {1, ...,n=|V|}, and another discrete structure over $V$, say a graph G, the problem of common intervals is to compute the induced subgraphs G[I], such that $I$ is an interval of [1, n] and G[I] satisfies some property Pi (as for example Pi= "being connected"). This kind of problems comes from comparative genomic in bioinformatics, mainly when the graph $G$ is a chain or a tree (Heber and Stoye 2001, Heber and Savage 2005, Bergeron et al 2008). When the family of intervals is closed under intersection, we present here the combination of two approaches, namely the idea of potential beginning developed in Uno, Yagiura 2000 and Bui-Xuan et al 2005 and the notion of generator as defined in Bergeron et al 2008. This yields a very simple generic algorithm to compute all common intervals, which gives optimal algorithms in various applications. For example in the case where $G$ is a tree, our framework yields the first linear time algorithms for the two properties: "being connected" and "being a path". In the case where $G$ is a chain, the problem is known as: common intervals of two permutations (Uno and Yagiura 2000), our algorithm provides not only the set of all common intervals but also with some easy modifications a tree structure that represents this set.