Related papers: Permutation patterns in genome rearrangement probl…

In this work, we consider a restricted case of the well studied Sorting by Block Interchanges problem. We put an upper bound k on the length of the blocks (substrings) to be interchanged at each step. We call the problem Sorting by k-Block…

Genomic distance between two genomes, i.e., the smallest number of genome rearrangements required to transform one genome into the other, is often used as a measure of evolutionary closeness of the genomes in comparative genomics studies.…

We consider two related problems arising from a question of R. Graham on quasirandom phenomena in permutation patterns. A ``pattern'' in a permutation $\sigma$ is the order type of the restriction of $\sigma : [n] \to [n]$ to a subset $S…

Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…

There are several approaches to study occurrences of consecutive patterns in permutations such as the inclusion-exclusion method, the tree representations of permutations, the spectral approach and others. We propose yet another approach to…

Let $k$ be a nonnegative integer, and let $\alpha$ and $\beta$ be two permutations of $n$ symbols. We say that $\alpha$ and $\beta$ $k$-commute if $H(\alpha\beta, \beta\alpha)=k$, where $H$ denotes the Hamming metric between permutations.…

In this paper, we present an algorithm that enumerates a certain class of signed permutations, referred to as grid signed permutation classes. In the case of permutations, the corresponding grid classes are of interest because they are…

We consider the problem of factoring permutations as a product of special types of transpositions, namely, those transpositions involving two positions with bounded distances. In particular, we investigate the minimum number, $\delta$, such…

We collect open problems in permutation patterns on four themes: rank-unimodality in the permutation pattern poset, Wilf-equivalence and shape-Wilf-equivalence, the enumeration of derangements in permutation classes, and sorting by stacks…

Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…

We enumerate permutations that avoid all but one of the $k$ patterns of length $k$ starting with a monotone increasing subsequence of length $k-1$. We compare the size of such permutation classes to the size of the class of permutations…

The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and…

Motivated by the problem of constructing bijective maps with low differential uniformity, we introduce the notion of permutation resemblance of a function, which looks to measure the distance a given map is from being a permutation. We…

We consider permutation classes having two basis elements of size three and one further basis element. We completely classify the possible enumeration sequences of such classes and demonstrate that there are far fewer of them than might be…

We investigate permutations in terms of their cycle structure and descent set. To do this, we generalize the classical bijection of Gessel and Reutenauer to deal with permutations that have some ascending and some descending blocks. We then…

Comtet introduced the notion of indecomposable permutations in 1972. A permutation is indecomposable if and only if it has no proper prefix which is itself a permutation. Indecomposable permutations were studied in the literature in various…

We define the operation of composing two hereditary classes of permutations using the standard composition of permutations as functions and we explore properties and structure of permutation classes considering this operation. We mostly…

We consider the problem of packing fixed-length patterns into a permutation, and develop a connection between the number of large patterns and the number of bonds in a permutation. Improving upon a result of Kaplansky and Wolfowitz, we…

Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…

We survey permutation-based methods for approximate k-nearest neighbor search. In these methods, every data point is represented by a ranked list of pivots sorted by the distance to this point. Such ranked lists are called permutations. The…