A geometric grid class consists of those permutations that can be drawn on a specified set of line segments of slope ±1 arranged in a rectangular pattern governed by a matrix. Using a mixture of geometric and language theoretic methods, we prove that such classes are specified by finite sets of forbidden permutations, are partially well ordered, and have… (More)
In this paper, we are interested in the combinatorial analysis of the whole genome duplication-random loss model of genome rearrangement initiated in  and . In this model, genomes composed of n genes are modelled by permutations of the set of integers [1..n], that can evolve through duplication-loss steps. It was previously shown that the class of… (More)
The goal of this paper is to present a brief survey of a collection of methods and results from the area of combinatorial search [1,8] focusing on graph reconstruction using queries of different type. The study is motivated by applications to genome sequencing.
LIAFA Motivations and the model Previous results Combinatorial properties Other questions Outline of the talk 1 Biological motivations and the combinatorial model 2 Previous results: the whole genome duplication-random loss model 3 Some combinatorial properties of the classes C(K , 1) and C(K , p) 4 Other questions to be considered Mathilde Bouvel A variant… (More)
In this paper, we give a polynomial (O(n 8)) algorithm for finding a longest common pattern between two permutations of size n given that one is separable. We also give an algorithm for general permutations whose complexity depends on the length of the longest simple permutation involved in one of our permutations.
A sequence of reversals that takes a signed permutation to the identity is perfect if at no step a common interval is broken. Determining a parsimonious perfect sequence of reversals that sorts a signed permutation is NP-hard. Here we show that, despite this worst-case analysis, with probability one, sorting can be done in polynomial time. Further, we find… (More)
This article presents a methodology that automatically derives a combinatorial specification for the permutation class C = Av(B), given its basis B of excluded patterns and the set of simple permutations in C, when these sets are both finite. This is achieved considering both pattern avoidance and pattern containment constraints in permutations. The… (More)
In this paper, we study the class of pin-permutations, that is to say of permutations having a pin representation. This class has been recently introduced in , where it is used to find properties (algebraicity of the generating function, decidability of membership) of classes of permutations, depending on the simple permutations this class contains. We… (More)