Genetic Algorithms, Operators, and DNA Fragment Assembly
Machine Learning - Special issue on applications in molecular biology
AMASS: a structured pattern matching approach to shotgun sequence assembly
AMASS: a structured pattern matching approach to shotgun sequence assembly
Cellular Genetic Algorithms
A new local search algorithm for the DNA fragment assembly problem
EvoCOP'07 Proceedings of the 7th European conference on Evolutionary computation in combinatorial optimization
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The sequencing process of a DNA chain for reading its components supposes a complex process, since only small DNA fragments can be read nowadays. Therefore, the use of optimization algorithms is required to rebuild a single chain from all the small pieces. We address here a simplified version of the problem, in which no errors in the sequencing process are allowed. The methods typically used in the literature for this problem are not satisfactory when solving realistic size instances, so there is a need for new more efficient and accurate methods. We propose a new iterated local search algorithm, highly competitive with the best algorithms in the literature, and considerably faster.