Approximating the number of double cut-and-join scenarios

DOI10.1016/J.TCS.2012.03.006MaRDI QIDQ441869zbMATH OpenOpenAlexFDO

Authors István Miklós, Eric Tannier

Publication date 8 August 2012

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2012.03.006

zbMATH Keywords

MCMCFPRASgenome rearrangementcomparative genomicsDCJ

Mathematics Subject Classification ID

Applications of graph theory (05C90) Genetics and epigenetics (92D10) Markov chains (discrete-time Markov processes on discrete state spaces) (60J10) Computational difficulty of problems (lower bounds, completeness, difficulty of approximation, etc.) (68Q17)

Recommendations

• Counting and sampling SCJ small parsimony solutions
• Distribution of genome rearrangement distance under double cut and join
• Finding Local Genome Rearrangements
• Weighted Minimum-Length Rearrangement Scenarios.
• A linear time approximation algorithm for the DCJ distance for genomes with bounded number of duplicates

Cites work

• scientific article; zbMATH DE number 1945172 (Why is no real title available?)
• Bayesian Phylogenetic Inference from Animal Mitochondrial Genome Arrangements
• Combinatorics of genome rearrangements.
• Equation of state calculations by fast computing machines
• Finding all sorting tandem duplication random loss operations
• Geometric bounds for eigenvalues of Markov chains
• Improved Bounds for Mixing Rates of Markov Chains and Multicommodity Flow
• Random generation of combinatorial structures from a uniform distribution

Cited in

(6)

• Weighted Minimum-Length Rearrangement Scenarios.
• Complexity and enumeration in models of genome rearrangement
• Counting and sampling SCJ small parsimony solutions
• Complexity and enumeration in models of genome rearrangement
• The genesis of the DCJ formula
• Distribution of genome rearrangement distance under double cut and join

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