scholarly journals GENOME HALVING WITH DOUBLE CUT AND JOIN

2007 ◽  
Author(s):  
ROBERT WARREN ◽  
DAVID SANKOFF
Keyword(s):  
Double Cut And Join

scholarly journals Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model

2019 ◽  
Vol 15 ◽  
pp. 117693431882053 ◽  
Author(s):  
Pavel Avdeyev ◽  
Shuai Jiang ◽  
Max A Alekseyev
Keyword(s):  
Approximate Solution ◽  
Original Problem ◽  
Approximation Error ◽  
Combinatorial Structure ◽  
Double Cut And Join ◽  
Linear Chromosomes ◽  
Circular Chromosomes ◽  
Relaxed Problem

Reconstruction of the median genome consisting of linear chromosomes from three given genomes is known to be intractable. There exist efficient methods for solving a relaxed version of this problem, where the median genome is allowed to have circular chromosomes. We propose a method for construction of an approximate solution to the original problem from a solution to the relaxed problem and prove a bound on its approximation error. Our method also provides insights into the combinatorial structure of genome transformations with respect to appearance of circular chromosomes.

scholarly journals Linear Time Additively Exact Algorithm for Transformation of Chain-Cycle Graphs for Arbitrary Costs of Deletions and Insertions

Mathematics ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. 2001
Author(s):  
Konstantin Gorbunov ◽  
Vassily Lyubetsky
Keyword(s):  
Linear Time ◽  
Exact Algorithm ◽  
Time Algorithm ◽  
Additive Constant ◽  
Weighted Graphs ◽  
Total Cost ◽  
Operation Costs ◽  
Double Cut And Join ◽  
Vertex Degrees ◽  
Directed Weighted Graphs

We propose a novel linear time algorithm which, given any directed weighted graphs a and b with vertex degrees 1 or 2, constructs a sequence of operations transforming a into b. The total cost of operations in this sequence is minimal among all possible ones or differs from the minimum by an additive constant that depends only on operation costs but not on the graphs themselves; this difference is small as compared to the operation costs and is explicitly computed. We assume that the double cut and join operations have identical costs, and costs of the deletion and insertion operations are arbitrary strictly positive rational numbers.

Genome Rearrangement by the Double Cut and Join Operation

2008 ◽  
pp. 385-416 ◽  
Author(s):  
Richard Friedberg ◽  
Aaron E. Darling ◽  
Sophia Yancopoulos
Keyword(s):  
Genome Rearrangement ◽  
Double Cut And Join

scholarly journals Approximating the number of Double Cut-and-Join scenarios

2012 ◽  
Vol 439 ◽  
pp. 30-40 ◽  
Author(s):  
István Miklós ◽  
Eric Tannier
Keyword(s):  
Double Cut And Join

scholarly journals Moments of genome evolution by Double Cut-and-Join

2015 ◽  
Vol 16 (S14) ◽  
Author(s):  
Priscila Biller ◽  
Laurent Guéguen ◽  
Eric Tannier
Keyword(s):  
Genome Evolution ◽  
Double Cut And Join

scholarly journals GENOME HALVING WITH DOUBLE CUT AND JOIN

2009 ◽  
Vol 07 (02) ◽  
pp. 357-371 ◽  
Author(s):  
ROBERT WARREN ◽  
DAVID SANKOFF
Keyword(s):  
General Context ◽  
Reciprocal Translocations ◽  
Double Cut And Join ◽  
Previous Algorithm ◽  
Circular Chromosomes

The genome halving problem, previously solved by El-Mabrouk for inversions and reciprocal translocations, is here solved in a more general context allowing transpositions and block interchange as well, for genomes including multiple linear and circular chromosomes. We apply this to several datasets and compare the results to the previous algorithm.

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