Rearrangement Models and Single-Cut Operations

Authors:
Paul Medvedev;Jens Stoye
Affiliations:
Department of Computer Science, University of Toronto,;Technische Fakultät, Universität Bielefeld, Germany
Venue:
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Year:
2009

Citing 16
Cited 0

On the problem of sorting burnt pancakes

Discrete Applied Mathematics
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals

Journal of the ACM (JACM)
Efficient algorithms for multichromosomal genome rearrangements

Journal of Computer and System Sciences - Computational biology 2002
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited

RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Edit Distances for Genome Comparisons Based on Non-Local Operations

CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
Transforming men into mice (polynomial algorithm for genomic distance problem)

FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Efficient sorting of genomic permutations by translocation, inversion and block interchange

Bioinformatics
Advances on sorting by reversals

Discrete Applied Mathematics
Genome rearrangements: a correct algorithm for optimal capping

Information Processing Letters
Whole genome duplications, multi-break rearrangements, and genome halving problem

SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Estimating true evolutionary distances under the DCJ model

Bioinformatics
HP Distance Via Double Cut and Join Distance

CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Genome Halving under DCJ Revisited

COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios

RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
SCJ: a variant of breakpoint distance for which sorting, genome median and genome halving problems are easy

WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
A unifying view of genome rearrangements

WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

There have been many widely used genome rearrangement models, such as reversals, Hannenhalli-Pevzner, and double-cut and join. Though each one can be precisely defined, the general notion of a model remains undefined. In this paper, we give a formal set-theoretic definition, which allows us to investigate and prove relationships between distances under various existing and new models. We also initiate the formal study of single-cut operations by giving a linear time algorithm for the distance problem under a new single-cut and join model.