The ABCs of MGR with DCJ

We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and reciprocal translocation, operations of transposition and bloc...

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Bibliographic Details
Published inEvolutionary bioinformatics online Vol. 4; p. 117693430800400
Main Authors Adam, Zaky, Sankoff, David
Format Journal Article
LanguageEnglish
Published London, England SAGE Publications 01.01.2008
Sage Publications Ltd
SAGE Publishing
Subjects
Bioinformatics
Blocking
Chloroplasts
Chromosomes
Evolutionary
Genomes
Inversions
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Summary:We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange. Empirically, with chloroplast and mammalian data sets, it finds solutions as good as or better than MGR when the latter operations are prohibited. Permitting these operations allows quantitatively better solutions where part of the reconstructed ancestral genomes may be included in circular chromosomes. We discuss the biological likelihood of transpositions and block interchanges in the mammalian data.
Bibliography:ObjectType-Article-2
SourceType-Scholarly Journals-1
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ISSN:1176-9343
1176-9343
DOI:10.1177/117693430800400004