Efficient sorting of genomic permutations by translocation, inversion and block interchange

  title={Efficient sorting of genomic permutations by translocation, inversion and block interchange},
  author={Sophia Yancopoulos and Oliver Attie and Richard Friedberg},
  volume={21 16},
MOTIVATION Finding genomic distance based on gene order is a classic problem in genome rearrangements. Efficient exact algorithms for genomic distances based on inversions and/or translocations have been found but are complicated by special cases, rare in simulations and empirical data. We seek a universal operation underlying a more inclusive set of evolutionary operations and yielding a tractable genomic distance with simple mathematical form. RESULTS We study a universal double-cut-and… 

Sorting permutations by cut-circularize-linearize-and-paste operations

BackgroundGenome rearrangements are studied on the basis of genome-wide analysis of gene orders and important in the evolution of species. In the last two decades, a variety of rearrangement

Sorting Linear Genomes with Rearrangements and Indels

  • M. D. BragaJ. Stoye
  • Biology
    IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • 2015
A very simple proof is presented showing that the distance, which can be computed in linear time, is the same for both the unrestricted and the restricted DCJ-indel models.

Sorting Signed Permutations by Inverse Tandem Duplication Random Losses

The algorithmic study of this new model of genome rearrangement, namely the inverse tandem duplication random loss (iTDRL) model, is initiated by proving that a shortest rearrangements scenario that transforms one given gene order into another given gene orders can be obtained in quasilinear time.

Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions

This paper provides a 1.5-approximation algorithm for sorting by weighted reversals, transpositions and inverted transposition for biologically realistic weights in order to reconstruct ancient events in the evolutionary history of organisms.

Sorting Permutations by Intergenic Operations

The signed reversal and transposition distance between two genomes considering their intergenic regions is investigated and two approximation algorithms are developed, which check how these algorithms behave when assigning weights for genome rearrangements.

Sorting by reversals, block interchanges, tandem duplications, and deletions

This paper presents a heuristic algorithm to sort an ancestral genome into a genome of a descendant (with arbitrary gene content) by reversals, block interchanges, tandem duplications, and deletions, where tandem duplication and deletion are of arbitrary size.

An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements

The preserving Genome Sorting Problem (pGSP) asks for a shortest sequence of rearrangement operations that transforms a given gene order into another given gene order by using rearrangement

Sorting by Weighted Reversals and Transpositions

This study studies the Sorting by Weighted Reversals and Transpositions problem on signed permutations and develops a generic approximation algorithm to deal with different weights for reversals and transpositions.

An Experimental Evaluation of Inversion-and Transposition-Based Genomic Distances through Simulations

The main finding is that inversion and DCJ measures return very similar results even on data generated using only transpositions, while the measure based on Hartman's bound is often too loose to provide comparable accuracy in genomic comparisons or phylogenetic reconstruction.

The Solution Space of Sorting by DCJ

An easy-to-compute formula is given that corresponds to the exact number of optimal DCJ sorting sequences for a particular subset of instances of the problem and the demonstration of the possibility of obtaining one optimal sorting sequence by properly replacing any pair of consecutive operations in another optimal sequence.



Sorting by Transpositions

The paper addresses the problem of genome comparison versus classical gene comparison and presents algorithms to analyze rearrangements in genomes evolving by transpositions and derive lower bounds on {\em transposition distance} between permutations and present approximation algorithms for sorting byTranspositions.

Genome rearrangements and sorting by reversals

  • V. BafnaP. Pevzner
  • Computer Science
    Proceedings of 1993 IEEE 34th Annual Foundations of Computer Science
  • 1993
It is demonstrated that the expected reversal distance is very close to the reversal diameter thereby indicating that reversal distance provides a good separation between related and non-related sequences.

Parametric genome rearrangement.

Two Notes on Genome Rearrangement

A family of signed permutations is described which proves a quadratic lower bound on the number of affected vertices in the overlap/interleaving graph during any optimal sorting scenario, which implies, in particular, an Omega(n3) lower bound for Bergeron's algorithm.

Polynomial-time Algorithm for Computing Translocation Distance Between Genomes

Genome rearrangements distance by fusion, fission, and transposition is easy

  • Zanoni DiasJ. Meidanis
  • Biology
    Proceedings Eighth Symposium on String Processing and Information Retrieval
  • 2001
Given two genomes represented as circularly ordered sequences of genes, this work shows a polynomial time algorithm for the minimum weight series of fusion, jissions, and transpositions that transforms one genome into the other.

An Efficient Algorithm for Sorting by Block-Interchanges and Its Application to the Evolution of Vibrio Species

This paper proposes a Omicron(deltan) time algorithm for solving the block-interchange distance problem by making use of permutation groups in algebra and implements it and applies it to the circular genomic sequences of three human vibrio pathogens for predicting their evolutionary relationships.

A new approach for approximating the transposition distance

This work studies the problem of computing the transposition distance between two linear gene orders, represented by permutations, and presents a very simple structure, the breakpoint diagram, and a 2.25-approximation algorithm for the problem based on this structure.

Working on the Problem of Sorting by Transpositions on Genome Rearrangements

This work implements the 1.5-approximation algorithm proposed by Christie for solving the problem of sorting by transpositions, introducing modifications to reduce its time complexity, and proposes heuristics to further improve its performance.

Sorting Permutations by Block-Interchanges