Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Reversal distance for partially ordered genomes
Bioinformatics
On the similarity of sets of permutations and its applications to genome comparison
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Stability of rearrangement measures in the comparison of genome sequences
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
HP Distance Via Double Cut and Join Distance
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Genome Halving under DCJ Revisited
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
Multichromosomal Genome Median and Halving Problems
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Sorting Genomes with Insertions, Deletions and Duplications by DCJ
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Rearrangement Phylogeny of Genomes in Contig Form
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
A new linear time algorithm to compute the genomic distance via the double cut and join distance
Theoretical Computer Science
Parking Functions, Labeled Trees and DCJ Sorting Scenarios
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Counting All DCJ Sorting Scenarios
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Rearrangement Models and Single-Cut Operations
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Parts of the problem of polyploids in rearrangement phylogeny
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Reactive stochastic local search algorithms for the genomic median problem
EvoCOP'08 Proceedings of the 8th European conference on Evolutionary computation in combinatorial optimization
WABI'09 Proceedings of the 9th 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 permutations by double-cut-and-joins
COCOON'10 Proceedings of the 16th annual international conference on Computing and combinatorics
Rearrangement Phylogeny of Genomes in Contig Form
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
The problem of chromosome reincorporation in DCJ sorting and halving
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Advances on genome duplication distances
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
On sorting genomes with DCJ and indels
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
On exploring genome rearrangement phylogenetic patterns
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
A practical algorithm for ancestral rearrangement reconstruction
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Bootstrapping phylogenies inferred from rearrangement data
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
GASTS: parsimony scoring under rearrangements
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Approximating the number of Double Cut-and-Join scenarios
Theoretical Computer Science
A simplified view of DCJ-indel distance
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
DCJ-indel distance with distinct operation costs
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Rearrangement-Based Phylogeny Using the Single-Cut-or-Join Operation
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Genome rearrangements have been modeled by a variety of operations such as inversions, translocations, fissions, fusions, transpositions and block interchanges. The double cut and join operation, introduced by Yancopoulos et al., allows to model all the classical operations while simplifying the algorithms. In this paper we show a simple way to apply this operation to the most general type of genomes with a mixed collection of linear and circular chromosomes. We also describe a graph structure that allows simplifying the theory and distance computation considerably, as neither capping nor concatenation of the linear chromosomes are necessary.