title: Algebraic double cut and join : A group-theoretic approach to the operator on multichromosomal genomes.
abstract: Establishing a distance between genomes is a significant problem in computational genomics, because its solution can be used to establish evolutionary relationships including phylogeny. The "double cut and join" (DCJ) model of chromosomal rearrangement proposed by Yancopoulos et al. (Bioinformatics 21:3340-3346, 2005) has received attention as it can model inversions, translocations, fusion and fission on a multichromosomal genome that may contain both linear and circular chromosomes. In this paper, we realize the DCJ operator as a group action on the space of multichromosomal genomes. We study this group action, deriving some properties of the group and finding group-theoretic analogues for the key results in the DCJ theory.
authors.affiliation: Centre for Research in Mathematics, University of Western Sydney, Penrith, NSW, 2751, Australia. s.bhatia@uws.edu.au.
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Bhatia
authors.affiliation: Centre for Research in Mathematics, University of Western Sydney, Penrith, NSW, 2751, Australia. a.egri-nagy@uws.edu.au.
authors.forename: Attila
authors.initials: A
authors.lastname: Egri-Nagy
authors.affiliation: Centre for Research in Mathematics, University of Western Sydney, Penrith, NSW, 2751, Australia. a.francis@uws.edu.au.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Francis
mesh_terms: D002875:Chromosomes / Q000235:genetics; D019143:Evolution, Molecular; D015321:Gene Rearrangement; D016678:Genome; D023281:Genomics; D055641:Mathematical Concepts; D008957:Models, Genetic; D010802:Phylogeny
keywords: Algebraic biology; Double cut and join; Genome rearrangements; Group theory; Inversion