Genomic distances under deletions and insertions
Theoretical Computer Science - Special papers from: COCOON 2003
Genome rearrangements and sorting by reversals
SFCS '93 Proceedings of the 1993 IEEE 34th Annual Foundations of Computer Science
A unifying view of genome rearrangements
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Genomic distance with DCJ and indels
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
On sorting genomes with DCJ and indels
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
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We extend the DCJ paradigm to perform genome rearrangments on pairs of genomes having unequal gene content and/or multiple copies by permitting genes in one genome which are completely or partially unmatched in the other. The existence of unmatched gene ends introduces new kinds of paths in the adjacency graph, since some paths can now terminate internal to a chromosome and not on telomeres. We introduce Òghost adjacenciesÓ to supply the missing gene ends in the genome not containing them. Ghosts enable us to close paths that were due to incomplete matching, just as null points enable us to close even paths terminating in telomeres. We define generalalized DCJ operations on the generalized adjacency graph, and give a prescription for calculating the DCJ distance for the expanded repertoire of operations which includes insertions, deletions and duplications.