Assignment of Orthologous Genes via Genome Rearrangement
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The solution space of sorting by reversals
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
A novel greedy algorithm for the minimum common string partition problem
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
On the minimum common integer partition problem
CIAC'06 Proceedings of the 6th Italian conference on Algorithms and Complexity
Approximating reversal distance for strings with bounded number of duplicates
MFCS'05 Proceedings of the 30th international conference on Mathematical Foundations of Computer Science
Minimum common string partition problem: hardness and approximations
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
Better approximations for the minimum common integer partition problem
APPROX'06/RANDOM'06 Proceedings of the 9th international conference on Approximation Algorithms for Combinatorial Optimization Problems, and 10th international conference on Randomization and Computation
Reversal distance for strings with duplicates: linear time approximation using hitting set
WAOA'06 Proceedings of the 4th international conference on Approximation and Online Algorithms
Parameterized Complexity
Parameterized Complexity and Biopolymer Sequence Comparison
The Computer Journal
Minimum common string partition revisited
FAW'10 Proceedings of the 4th international conference on Frontiers in algorithmics
Scaffold filling under the breakpoint distance
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Filling scaffolds with gene repetitions: maximizing the number of adjacencies
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Exponential and polynomial time algorithms for the minimum common string partition problem
COCOA'11 Proceedings of the 5th international conference on Combinatorial optimization and applications
Minimum common string partition revisited
Journal of Combinatorial Optimization
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Minimum Common String Partition (MCSP) and related problems are of interest in, e.g., comparative genomics, DNA fingerprint assembly, and ortholog assignment. Given two strings with equal symbol content, the problem is to partition one string into kblocks, kas small as possible, and to permute them so as to obtain the other string. MCSP is NP-hard, and only approximation algorithms are known. Here we show that MCSP is fixed-parameter tractable in suitable parameters, so that practical instances can be efficiently solved to optimality.