An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes

2015 ◽  
Vol 22 (5) ◽  
pp. 425-435 ◽  
Author(s):  
Mingfu Shao ◽  
Yu Lin ◽  
Bernard M.E. Moret
Keyword(s):  
Exact Algorithm ◽  
Duplicate Genes ◽  
Double Cut And Join

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.

Exact algorithm for generating optimal homogenous strip T-shape layouts

2013 ◽  
Vol 32 (9) ◽  
pp. 2634-2637
Author(s):  
Jun JI ◽  
Yi-ping LU ◽  
Jian-zhong ZHA ◽  
Yao-dong CUI
Keyword(s):  
Exact Algorithm

scholarly journals An exact algorithm for subgraph homeomorphism

2009 ◽  
Vol 7 (4) ◽  
pp. 464-468 ◽  
Author(s):  
Andrzej Lingas ◽  
Martin Wahlen
Keyword(s):  
Exact Algorithm

scholarly journals A Comparison of Genetic Representations and Initialisation Methods for the Multi-objective Shortest Path Problem on Multigraphs

2021 ◽  
Vol 2 (3) ◽  
Author(s):  
Lilla Beke ◽  
Michal Weiszer ◽  
Jun Chen
Keyword(s):  
Shortest Path ◽  
Time Budget ◽  
Exact Algorithm ◽  
Simple Graph ◽  
Shortest Path Problem ◽  
Future Application ◽  
Multi Objective ◽  
Trade Offs ◽  
Conflicting Objectives ◽  
Problem Instances

AbstractThis paper compares different solution approaches for the multi-objective shortest path problem (MSPP) on multigraphs. Multigraphs as a modelling tool are able to capture different available trade-offs between objectives for a given section of a route. For this reason, they are increasingly popular in modelling transportation problems with multiple conflicting objectives (e.g., travel time and fuel consumption), such as time-dependent vehicle routing, multi-modal transportation planning, energy-efficient driving, and airport operations. The multigraph MSPP is more complex than the NP-hard simple graph MSPP. Therefore, approximate solution methods are often needed to find a good approximation of the true Pareto front in a given time budget. Evolutionary algorithms have been successfully applied for the simple graph MSPP. However, there has been limited investigation of their applications to the multigraph MSPP. Here, we extend the most popular genetic representations to the multigraph case and compare the achieved solution qualities. Two heuristic initialisation methods are also considered to improve the convergence properties of the algorithms. The comparison is based on a diverse set of problem instances, including both bi-objective and triple objective problems. We found that the metaheuristic approach with heuristic initialisation provides good solutions in shorter running times compared to an exact algorithm. The representations were all found to be competitive. The results are encouraging for future application to the time-constrained multigraph MSPP.

Systematic evidence from gene duplication and regulation

1990 ◽  
Vol 3 (1) ◽  
pp. 145
Author(s):  
DJ Colgan
Keyword(s):  
Gene Duplication ◽  
Evolutionary History ◽  
Tandem Duplication ◽  
Fragment Length Polymorphism ◽  
Duplicate Genes ◽  
Polymorphism Analysis ◽  
Multiple Origins ◽  
The Family ◽  
History Of ◽  
Phylogenetic Hypotheses

This paper is a review of the use of information regarding the presence of duplicate genes and their regulation in systematics. The review concentrates on data derived from protein electrophoresis and restriction fragment length polymorphism analysis. The appearance of a duplication in a subset of a group of species implies that the members of the subset belong to the same clade. Suppression of the duplication may render this clade apparently paraphyletic, but may itself be informative of relations within the lineage through patterns of loss of expression in all, or some tissues, or through restrictions of the formation of functional heteropolymers in polymeric enzymes. Examples are given of studies which have used such information to establish phylogenetic hypotheses at the family level, to identify an auto- or allo-polyploid origin of polyploid species and to determine whether there have been single or multiple origins of such species. The likelihood of homoplasy in the patterns of appearance and regulation of duplicates depends on the molecular basis of the duplication. In particular, the contrast between the expected consequences of tandem duplication and the expression of pseudogenes emphasises the value of determining the mechanism of the original duplication. Many instances of sporadic gene duplication are now known, and polyploidisation is a common event in the evolutionary history of both plants and animals. So the opportunities to discover duplicationrelated characters will arise in many systematic studies. A program is presented to increase the chances that such useful information will be recognisable during the studies.

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