Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
Minimum Common String Partition Parameterized
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
The greedy algorithm for edit distance with moves
Information Processing Letters
Minimum common string partition revisited
FAW'10 Proceedings of the 4th international conference on Frontiers in algorithmics
Minimum common string partition problem: hardness and approximations
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
Parameterized Complexity
Filling scaffolds with gene repetitions: maximizing the number of adjacencies
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Minimum common string partition revisited
Journal of Combinatorial Optimization
An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivated by the trend of genome sequencing without completing the sequence of the whole genomes, Muñoz et al. recently studied the problem of filling an incomplete multichromosomal genome (or scaffold) I with respect to a complete target genome G such that the resulting genomic distance between I′ and G is minimized, where I′ is the corresponding filled scaffold. We call this problem the one-sided scaffold filling problem. In this paper, we follow Muñoz et al. to investigate the scaffold filling problem under the breakpoint distance for the simplest unichromosomal genomes.When the input genome contains no gene repetition (i.e., is a fragment of a permutation), we show that the two-sided scaffold filling problem is polynomially solvable. However, when the input genome contains some genes which appear twice, even the one-sided scaffold filling problem becomes NP-complete. Finally, using the ideas for solving the two-sided scaffold filling problem under the breakpoint distance we show that the two-sided scaffold filling problem under the genomic/rearrangement distance is also polynomially solvable.