Perfect Sorting by Reversals Is Not Always Difficult
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Whole genome duplications, multi-break rearrangements, and genome halving problem
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Consensus Genetic Maps as Median Orders from Inconsistent Sources
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multi-break rearrangements and chromosomal evolution
Theoretical Computer Science
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
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the 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
A Fast and Exact Algorithm for the Median of Three Problem--A Graph Decomposition Approach
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
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
Multi-break rearrangements: from circular to linear genomes
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)
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
Scaffold filling under the breakpoint distance
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
Limited lifespan of fragile regions in mammalian evolution
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
The transposition median problem is NP-complete
Theoretical Computer Science
Weighted genomic distance can hardly impose a bound on the proportion of transpositions
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Filling scaffolds with gene repetitions: maximizing the number of adjacencies
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
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
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
A unifying view of genome rearrangements
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Paths and cycles in breakpoint graphs of random multichromosomal genomes
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Ordering partially assembled genomes using gene arrangements
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
A PQ framework for reconstructions of common ancestors and phylogeny
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Rearrangement of noisy genomes
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Approximating the number of Double Cut-and-Join scenarios
Theoretical Computer Science
Scaffold Filling under the Breakpoint and Related Distances
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The complexity of string partitioning
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
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
Tandem halving problems by DCJ
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inapproximability of (1,2)-Exemplar Distance
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Finding genomic distance based on gene order is a classic problem in genome rearrangements. Efficient exact algorithms for genomic distances based on inversions and/or translocations have been found but are complicated by special cases, rare in simulations and empirical data. We seek a universal operation underlying a more inclusive set of evolutionary operations and yielding a tractable genomic distance with simple mathematical form. Results: We study a universal double-cut-and-join operation that accounts for inversions, translocations, fissions and fusions, but also produces circular intermediates which can be reabsorbed. The genomic distance, computable in linear time, is given by the number of breakpoints minus the number of cycles (b-c) in the comparison graph of the two genomes; the number of hurdles does not enter into it. Without changing the formula, we can replace generation and re-absorption of a circular intermediate by a generalized transposition, equivalent to a block interchange, with weight two. Our simple algorithm converts one multi-linear chromosome genome to another in the minimum distance. Contact: syancopo@nshs.edu