An asymmetric approach to preserve common intervals while sorting by reversals

Dias Vieira Braga M, Gautier C, Sagot M-F. An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms for Molecular Biology. 2009;4(1):16.Background: The reversal distance and optimal sequences of reversals to transform a genome into another are useful tools to analyse evolutionary scenarios. However, the number of sequences is huge and some additional criteria should be used to obtain a more accurate analysis. One strategy is searching for sequences that respect constraints, such as the common intervals (clusters of co-localised genes). Another approach is to explore the whole space of sorting sequences, eventually grouping them into classes of equivalence. Recently both strategies started to be put together, to restrain the space to the sequences that respect constraints. In particular an algorithm has been proposed to list classes whose sorting sequences do not break the common intervals detected between the two inital genomes A and B. This approach may reduce the space of sequences and is symmetric (the result of the analysis sorting A into B can be obtained from the analysis sorting B into A). Results: We propose an alternative approach to restrain the space of sorting sequences, using progressive instead of initial detection of common intervals (the list of common intervals is updated after applying each reversal). This may reduce the space of sequences even more, but is shown to be asymmetric. Conclusions: We suggest that our method may be more realistic when the relation ancestor-descendant between the analysed genomes is clear and we apply it to do a better characterisation of the evolutionary scenario of the bacterium Rickettsia felis with respect to one of its ancestors

Average-case analysis of perfect sorting by reversals (Journal Version)

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any common interval. B\'erard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals. Combinatorial properties of this family of trees are essential to the algorithm analysis. Here, we use the expected value of certain tree parameters to prove that the average run-time of the algorithm is at worst, polynomial, and additionally, for sufficiently long permutations, the sorting algorithm runs in polynomial time with probability one. Furthermore, our analysis of the subclass of commuting scenarios yields precise results on the average length of a reversal, and the average number of reversals.Comment: A preliminary version of this work appeared in the proceedings of Combinatorial Pattern Matching (CPM) 2009. See arXiv:0901.2847; Discrete Mathematics, Algorithms and Applications, vol. 3(3), 201

Parking functions, labeled trees and DCJ sorting scenarios

In genome rearrangement theory, one of the elusive questions raised in recent years is the enumeration of rearrangement scenarios between two genomes. This problem is related to the uniform generation of rearrangement scenarios, and the derivation of tests of statistical significance of the properties of these scenarios. Here we give an exact formula for the number of double-cut-and-join (DCJ) rearrangement scenarios of co-tailed genomes. We also construct effective bijections between the set of scenarios that sort a cycle and well studied combinatorial objects such as parking functions and labeled trees.Comment: 12 pages, 3 figure

Polynomial-time sortable stacks of burnt pancakes

Pancake flipping, a famous open problem in computer science, can be formalised as the problem of sorting a permutation of positive integers using as few prefix reversals as possible. In that context, a prefix reversal of length k reverses the order of the first k elements of the permutation. The burnt variant of pancake flipping involves permutations of signed integers, and reversals in that case not only reverse the order of elements but also invert their signs. Although three decades have now passed since the first works on these problems, neither their computational complexity nor the maximal number of prefix reversals needed to sort a permutation is yet known. In this work, we prove a new lower bound for sorting burnt pancakes, and show that an important class of permutations, known as "simple permutations", can be optimally sorted in polynomial time.Comment: Accepted pending minor revisio

A survey on algorithmic aspects of modular decomposition

The modular decomposition is a technique that applies but is not restricted to graphs. The notion of module naturally appears in the proofs of many graph theoretical theorems. Computing the modular decomposition tree is an important preprocessing step to solve a large number of combinatorial optimization problems. Since the first polynomial time algorithm in the early 70's, the algorithmic of the modular decomposition has known an important development. This paper survey the ideas and techniques that arose from this line of research

On the effective and automatic enumeration of polynomial permutation classes

We describe an algorithm, implemented in Python, which can enumerate any permutation class with polynomial enumeration from a structural description of the class. In particular, this allows us to find formulas for the number of permutations of length n which can be obtained by a finite number of block sorting operations (e.g., reversals, block transpositions, cut-and-paste moves)