1 research outputs found
A general method for common intervals
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 , say a graph G, the
problem of common intervals is to compute the induced subgraphs G[I], such that
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 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 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 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