Related papers: Sorting by Transpositions is Difficult
Given a signed permutation on $n$ elements, we need to sort it with the fewest reversals. This is a fundamental algorithmic problem motivated by applications in comparative genomics, as it allows to accurately model rearrangements in small…
A consecutive pattern in a permutation $\pi$ is another permutation $\sigma$ determined by the relative order of a subsequence of contiguous entries of $\pi$. Traditional notions such as descents, runs and peaks can be viewed as particular…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
An algorithm is presented for unranking permutations in transposition order: Given a seed s\in N, the algorithm produces a permutation P(s) that differs from the permutation P(s+1) by the transposition of two elements.
The subject of pattern avoiding permutations has its roots in computer science, namely in the problem of sorting a permutation through a stack. A formula for the number of permutations of length n that can be sorted by passing it twice…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
We give a positive answer to a question raised by Davis et al. ({\em Discrete Mathematics} 341, 2018), concerning permutations with the same pinnacle set. Given $\pi\in S_n$, a {\em pinnacle} of $\pi$ is an element $\pi_i$ ($i\neq 1,n$)…
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…
We consider the following general model of a sorting procedure: we fix a hereditary permutation class $\mathcal{C}$, which corresponds to the operations that the procedure is allowed to perform in a single step. The input of sorting is a…
We give a bijection between permutations of length 2n and certain pairs of Dyck paths with labels on the down steps. The bijection arises from a game in which two players alternate selecting from a set of 2n items: the permutation encodes…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…
Given a countable set X (usually taken to be N or Z), an infinite permutation $\pi$ of X is a linear ordering $<_\pi$ of X. This paper investigates the combinatorial complexity of infinite permutations on N associated with the image of…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
Permutations are usually enumerated by size, but new results can be found by enumerating them by inversions instead, in which case one must restrict one's attention to indecomposable permutations. In the style of the seminal paper by Simion…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
We present a deterministic comparison-based algorithm that sorts sequences avoiding a fixed permutation $\pi$ in linear time, even if $\pi$ is a priori unkown. Moreover, the dependence of the multiplicative constant on the pattern $\pi$…
We study the duplication with transposition distance between strings of length $n$ over a $q$-ary alphabet and their roots. In other words, we investigate the number of duplication operations of the form $x = (abcd) \to y = (abcbd)$, where…
Sorting is a fundamental operation of all computer systems, having been a long-standing significant research topic. Beyond the problem formulation of traditional sorting algorithms, we consider sorting problems for more abstract yet…
A descent $k$ of a permutation $\pi=\pi_{1}\pi_{2}\dots\pi_{n}$ is called a big descent if $\pi_{k}>\pi_{k+1}+1$; denote the number of big descents of $\pi$ by $\operatorname{bdes}(\pi)$. We study the distribution of the…