Genetic Algorithm Approach for the Closest String Problem
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
On the Structure of Small Motif Recognition Instances
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
A data-based coding of candidate strings in the closest string problem
Proceedings of the 11th Annual Conference Companion on Genetic and Evolutionary Computation Conference: Late Breaking Papers
Consensus Optimizing Both Distance Sum and Radius
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Ant-CSP: An Ant Colony Optimization Algorithm for the Closest String Problem
SOFSEM '10 Proceedings of the 36th Conference on Current Trends in Theory and Practice of Computer Science
Hard problems in similarity searching
Discrete Applied Mathematics
Complexities of the centre and median string problems
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Finding optimal alignment and consensus of circular strings
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Exact algorithm and heuristic for the Closest String Problem
Computers and Operations Research
A GRASP algorithm for the Closest String Problem using a probability-based heuristic
Computers and Operations Research
The bounded search tree algorithm for the closest string problem has quadratic smoothed complexity
MFCS'11 Proceedings of the 36th international conference on Mathematical foundations of computer science
Approximations and partial solutions for the consensus sequence problem
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
A parameterized complexity tutorial
LATA'12 Proceedings of the 6th international conference on Language and Automata Theory and Applications
A basic parameterized complexity primer
The Multivariate Algorithmic Revolution and Beyond
Enumerating neighbour and closest strings
IPEC'12 Proceedings of the 7th international conference on Parameterized and Exact Computation
Configurations and minority in the string consensus problem
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
Finding consensus and optimal alignment of circular strings
Theoretical Computer Science
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CLOSEST STRING is one of the core problems in the field of consensus word analysis with particular importance for computational biology. Given k strings of same length and a positive integer d, find a "closest string" s such that none of the given strings has Hamming distance greater than d from s. Closest String is NP-complete. We show how to solve CLOSEST STRING in linear time for constant d (the exponential growth is O(d d . We extend this result to the closely related problems d-MISMATCH and DISTINGUISHING STRING SELECTION. Moreover, we discuss fixed parameter tractability for parameter k and give an efficient linear time algorithm for CLOSEST STRING when k = 3. Finally, the practical usefulness of our findings is substantiated by some experimental results.