Evolutionary algorithms in theory and practice: evolution strategies, evolutionary programming, genetic algorithms
SIAM Journal on Discrete Mathematics
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Of mice and men: algorithms for evolutionary distances between genomes with translocation
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Grasp and Path Relinking for 2-Layer Straight Line Crossing Minimization
INFORMS Journal on Computing
Reactive GRASP: An Application to a Matrix Decomposition Problem in TDMA Traffic Assignment
INFORMS Journal on Computing
A Hybrid GRASP with Perturbations for the Steiner Problem in Graphs
INFORMS Journal on Computing
Parallel GRASP with path-relinking for job shop scheduling
Parallel Computing - Special issue: Parallel computing in numerical optimization
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
A 1.375-Approximation Algorithm for Sorting by Transpositions
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A very elementary presentation of the Hannenhalli-Pevzner theory
Discrete Applied Mathematics
A simulation tool for the study of symmetric inversions in bacterial genomes
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Sorting by transpositions is difficult
ICALP'11 Proceedings of the 38th international colloquim conference on Automata, languages and programming - Volume Part I
A 2-approximation algorithm for sorting by prefix reversals
ESA'05 Proceedings of the 13th annual European conference on Algorithms
The median problem for the reversal distance in circular bacterial genomes
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Sorting genomes using almost-symmetric inversions
Proceedings of the 27th Annual ACM Symposium on Applied Computing
MFCS'12 Proceedings of the 37th international conference on Mathematical Foundations of Computer Science
A hybrid GRASP heuristic to construct effective drawings of proportional symbol maps
Computers and Operations Research
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Genome Rearrangement is a field that addresses the problem of finding the minimum number of global operations that transform one given genome into another. In this work we develop an algorithm for three constrained versions of the event called inversion, which occurs when a chromosome breaks at two locations called breakpoints and the DNA between the breakpoints is reversed. The constrained versions are called symmetric, almost-symmetric and unitary inversions. In this paper, we present a greedy randomized search procedure to find the minimum number of such operations between two genomes. Our approach is, to our knowledge, the first genome rearrangement problem modeled using this metaheuristic. Our model is an iterative process in which each iteration receives a feasible solution whose neighborhood is investigated for a better solution. This search uses greediness to shape the candidate list and randomness to select elements from the list. A previous greedy heuristic was used as an initial solution. In almost every case, we were able to improve that initial solution by providing a new sequence of inversions that uses less operations. For permutations of size 10, our solutions were, on average, 5 inversions shorter than the initial solution. For permutations of size 15 and 20, our solutions were, on average, 10 and 16 inversions shorter than the initial solution, respectively. For longer permutations ranging from 25 to 50 elements, we generated solutions that were, on average, 20--22 inversions shorter than the initial solution. We believe that the method proposed in this work can be adjusted to other genome rearrangement problems.