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Genome rearrangements have been modeled by a variety of operations such as inversions, translocations, fissions, fusions, transpositions and block interchanges. The double cut and join operation, introduced by Yancopoulos et al., allows to model all the classical operations while simplifying the algorithms. In this paper we show a simple way to apply this… (More)

The study of genome rearrangements is an important tool in comparative genomics. This paper revisits the problem of sorting a multichromosomal genome by translocations, i.e., exchanges of chromosome ends. We give an elementary proof of the formula for computing the translocation distance in linear time, and we give a new algorithm for sorting by… (More)

The genomic distance problem in the Hannenhalli-Pevzner (HP) theory is the following: Given two genomes whose chromosomes are linear, calculate the minimum number of translocations, fusions, fissions and inversions that transform one genome into the other. This paper presents a new distance formula based on a simple tree structure that captures all the… (More)

This paper presents an elementary proof of the Hannenhalli-Pevzner theorem on the reversal distance of two signed permutations. It uses a single PQ-tree to encode the various features of a permutation. The parameters called hurdles and fortress are replaced by a single one, whose value is computed by a simple and efficient algorithm.

Whole genome comparison based on gene order has become a popular approach in comparative genomics. An important task in this field is the detection of gene clusters, i.e., sets of genes that occur co-localized in several genomes. For most applications, it is preferable to extend this definition to allow for small deviations in the gene content of the… (More)

In the past years, many combinatorial arguments have been made to support the theory that mammalian genome rearrangement scenarios rely heavily on breakpoint reuse. Different models of genome rearrangements have been suggested, from the classical set of operations that include inversions, translocations, fusions and fissions, to more elaborate models that… (More)

- Cedric Chauve, Yoan Diekmann, Steffen Heber, Julia Mixtacki, Sven Rahmann, Jens Stoye +9 others
- 2006

The information that groups of genes co-occur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene clusters, has led to various models of increasing generality. A central feature to enhance the biological relevance of their definition when applied to real genomic… (More)

The genomic distance problem in the Hannenhalli-Pevzner theory is the following: Given two genomes whose chromosomes are linear , calculate the minimum number of inversions and translocations that transform one genome into the other. This paper presents a new distance formula based on a simple tree structure that captures all the delicate features of this… (More)

- OLIVIER GASCUEL, Andrew Meade, Anne Bergeron, Bernard Moret, David Bryant, David Sankoff +17 others
- 2004

Mathematics of Evolution and Phylogeny Oliv: " fm " — 2004/11/16 — 22:56 — page ii — #2 Oliv: " fm " — 2004/11/16 — 22:56 — page iii — #3 1 Oliv: " fm " — 2004/11/16 — 22:56 — page iv — #4 3 Great Clarendon Street, Oxford ox2 6dp Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in… (More)

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