Related papers: Estimating Genome Reversal Distance by Genetic Alg…
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…
In 1937, biologists Sturtevant and Tan posed a computational question: transform a chromosome represented by a permutation of genes, into a second permutation, using a minimum-length sequence of reversals, each inverting the order of a…
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…
Sorting a permutation by reversals is a famous problem in genome rearrangements. Since 1997, quite some biological evidence were found that in many genomes the reversed regions are usually flanked by a pair of inverted repeats. This type of…
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…
Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…
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…
In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of genes in a genome. The transposition distance, that is, the minimum number of transpositions needed to transform a genome into another, is,…
In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These…
A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…
Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the…
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…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
The experimenter must perform a legitimate search in the entire set of feasible censoring schemes to identify the optimal type II progressive censoring scheme, when applied to a life-testing experiment. Current recommendations are limited…
Computing the reversal distances of signed permutations is an important topic in Bioinformatics. Recently, a new lower bound for the reversal distance was obtained via the plane permutation framework. This lower bound appears different from…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…