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A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance

Authors: Anne Bergeron, Julia Mixtacki, and Jens Stoye

Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)

Abstract

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. We will present a new distance formula based on a simple tree structure that captures all the delicate features of this problem in a unifying way, and a linear-time algorithm for computing this distance.

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Anne Bergeron, Julia Mixtacki, and Jens Stoye. A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{bergeron_et_al:DagSemProc.10231.2,
  author =	{Bergeron, Anne and Mixtacki, Julia and Stoye, Jens},
  title =	{{A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance}},
  booktitle =	{Structure Discovery in Biology: Motifs, Networks \& Phylogenies},
  pages =	{1--25},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10231},
  editor =	{Alberto Apostolico and Andreas Dress and Laxmi Parida},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.2},
  URN =		{urn:nbn:de:0030-drops-26892},
  doi =		{10.4230/DagSemProc.10231.2},
  annote =	{Keywords: Comparative genomics, genomic distance computation, HP theory}
}

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A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance

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