Related papers: Sorting by Transpositions is Difficult
The Transposition Distance Problem (TDP) is a classical problem in genome rearrangements which seeks to determine the minimum number of transpositions needed to transform a linear chromosome into another represented by the permutations…
One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements…
In genome rearrangements, the mutational event transposition swaps two adjacent blocks of genes in one chromosome. The Transposition Distance Problem (TDP) aims to find the minimum number of transpositions required to transform one…
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…
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…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
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…
A number of fields, including the study of genome rearrangements and the design of interconnection networks, deal with the connected problems of sorting permutations in "as few moves as possible", using a given set of allowed operations, or…
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…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
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…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
We consider the problem of upper bounding the number of circular transpositions needed to sort a permutation. It is well known that any permutation can be sorted using at most $n(n-1)/2$ adjacent transpositions. We show that, if we allow…
We consider the number of passes a permutation needs to take through a stack if we only pop the appropriate output values and start over with the remaining entries in their original order. We define a permutation $\pi$ to be $k$-pass…
The set of all permutations with $n$ symbols is a symmetric group denoted by $S_n$. A transposition tree, $T$, is a spanning tree over its $n$ vertices $V_T=${$1, 2, 3, \ldots n$} where the vertices are the positions of a permutation $\pi$…
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…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
A wide range of applications, most notably in comparative genomics, involve the computation of a shortest sorting sequence of operations for a given permutation, where the set of allowed operations is fixed beforehand. Such sequences are…