Rearrangement models and single-cut operations

Anne Bergeron, Paul Medvedev, Jens Stoye

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

There have been many widely used genome rearrangement models, such as reversals, Hannenhalli-Pevzner (HP), 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. Among our results is that sorting in the HP model is equivalent to sorting in the reversal model when the initial and final genomes are linear uni-chromosomal. 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.

Original languageEnglish (US)
Pages (from-to)1213-1225
Number of pages13
JournalJournal of Computational Biology
Volume17
Issue number9
DOIs
StatePublished - Sep 1 2010

All Science Journal Classification (ASJC) codes

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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