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Computing the family-free DCJ similarity | BMC Bioinformatics | Full Text
2018年5月8日 · We propose an exact ILP algorithm to solve the family-free DCJ similarity problem, then we show its APX-hardness and present four combinatorial heuristics with …
Genome Rearrangement by the Double Cut and Join Operation
Recently, attention has been given to a single universal operation, the double cut and join (DCJ), which acts indiscriminately on gene ends without regard to the chromosomal disposition of the …
On the family-free DCJ distance and similarity
2015年4月1日 · In this work we propose the problem of computing the DCJ distance of two given genomes without prior gene family assignment, directly using the pairwise similarities between …
DCJ-indel and DCJ-substitution distances with distinct operation …
2013年7月23日 · In the present study we extend the DCJ-indel and the DCJ-substitution models, considering that the content-modifying cost is distinct from and upper bounded by the DCJ …
Algebraic double cut and join | Journal of Mathematical Biology
2014年12月11日 · The “double cut and join” (DCJ) model of chromosomal rearrangement proposed by Yancopoulos et al. (Bioinformatics 21:3340–3346, 2005) has received attention …
DCJ-RNA - double cut and join for RNA secondary structures
2017年10月16日 · This paper proposes a double cut and join for RNA secondary structures (DCJ-RNA) algorithm. This algorithm allows for the description of evolutionary scenarios that are …
An Exact Algorithm to Compute the DCJ Distance for Genomes …
2014年12月17日 · In this article, we propose an integer linear programming (ILP) formulation to compute the DCJ distance between two genomes with duplicate genes. We also provide an …
Algorithms for sorting unsigned linear genomes by the DCJ
2011年2月1日 · In this article, we study the problem of computing the DCJ distance on two unsigned linear multichromosomal genomes (abbreviated as UDCJ). Results: We devise a 1.5 …
Approximating the double-cut-and-join distance between …
2011年10月5日 · Given two unsigned genomes A and B on the same set of genes, the problem of sorting unsigned genomes by DCJ operations (UDCJ) is defined to find a shortest sequence of …