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In the minimum common string partition (MCSP) problem two related input strings are given. “Related” refers to the property that both strings consist of the same set of letters appearing the same number of times in each of the two strings. The MCSP seeks a minimum cardinality partitioning of one string into non-overlapping substrings that is also a valid partitioning for the second string. This problem...
The most strings with few bad columns problem is an NP-hard combinatorial optimization problem from the bioinformatics field. This paper presents the first integer linear programming model for this problem. Moreover, a simple greedy heuristic and a more sophisticated extension, namely a greedy-based pilot method, are proposed. Experiments show that, as expected, the greedy-based pilot method improves...
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