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

The distribution of cycles in breakpoint graphs of signed permutations

Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of those cycles is therefore critical to gaining insight on the distributions of the genomic distances that rely on it. We extend here the work initiated by Doignon and Labarre, who enumerated unsigned permutations whose breakpoint graph contains $k$ cycles, to signed permutations, and prove explicit formulas for computing the expected value and the variance of the corresponding distributions, both in the unsigned case and in the signed case. We also compare these distributions to those of several well-studied distances, emphasising the cases where approximations obtained in this way stand out. Finally, we show how our results can be used to derive simpler proofs of other previously known results

Degenerate crossing number and signed reversal distance

The degenerate crossing number of a graph is the minimum number of transverse crossings among all its drawings, where edges are represented as simple arcs and multiple edges passing through the same point are counted as a single crossing. Interpreting each crossing as a cross-cap induces an embedding into a non-orientable surface. In 2007, Mohar showed that the degenerate crossing number of a graph is at most its non-orientable genus and he conjectured that these quantities are equal for every graph. He also made the stronger conjecture that this also holds for any loopless pseudotriangulation with a fixed embedding scheme. In this paper, we prove a structure theorem that almost completely classifies the loopless 2-vertex embedding schemes for which the degenerate crossing number equals the non-orientable genus. In particular, we provide a counterexample to Mohar's stronger conjecture, but show that in the vast majority of the 2-vertex cases, the conjecture does hold. The reversal distance between two signed permutations is the minimum number of reversals that transform one permutation to the other one. If we represent the trajectory of each element of a signed permutation under successive reversals by a simple arc, we obtain a drawing of a 2-vertex embedding scheme with degenerate crossings. Our main result is proved by leveraging this connection and a classical result in genome rearrangement (the Hannenhali-Pevzner algorithm) and can also be understood as an extension of this algorithm when the reversals do not necessarily happen in a monotone order.Comment: Appears in the Proceedings of the 31st International Symposium on Graph Drawing and Network Visualization (GD 2023

Genome dedoubling by DCJ and reversal

<p>Abstract</p> <p>Background</p> <p>Segmental duplications in genomes have been studied for many years. Recently, several studies have highlighted a biological phenomenon called <it>breakpoint-duplication</it> that apparently associates a significant proportion of segmental duplications in Mammals, and the Drosophila species group, to breakpoints in rearrangement events.</p> <p>Results</p> <p>In this paper, we introduce and study a combinatorial problem, inspired from the breakpoint-duplication phenomenon, called the <it>Genome Dedoubling Problem.</it> It consists of finding a minimum length rearrangement scenario required to transform a genome with duplicated segments into a non-duplicated genome such that duplications are caused by rearrangement breakpoints. We show that the problem, in the Double-Cut-and-Join (DCJ) and the reversal rearrangement models, can be reduced to an APX-complete problem, and we provide algorithms for the Genome Dedoubling Problem with 2-approximable parts. We apply the methods for the reconstruction of a non-duplicated ancestor of <it>Drosophila yakuba.</it></p> <p>Conclusions</p> <p>We present the <it>Genome Dedoubling Problem</it>, and describe two algorithms solving the problem in the DCJ model, and the reversal model. The usefulness of the problems and the methods are showed through an application to real Drosophila data.</p