Abstract
We propose a local-search based algorithm to design DNA sequence sets that satisfy several combinatorial constraints about hamming-distance criteria. To deal with the constraints in the local search, we adopt elaborate (and dynamic) neighborhood search frameworks called the Variable Neighborhood Search (VNS) and the Variable Depth Search (VDS). Although our algorithm can deal with many types of hamming distance-based constraints and is easy to extend (e.g., also applicable for other constraints), in computational experiments, we succeeded in generating better sequence sets than the ones generated by exiting methods of more specified constraints.
This research partly received financial support from Scientific research fund of Ministry of Education, Culture, Sports, Science and Technology.
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Kawashimo, S., Ono, H., Sadakane, K., Yamashita, M. (2006). DNA Sequence Design by Dynamic Neighborhood Searches. In: Mao, C., Yokomori, T. (eds) DNA Computing. DNA 2006. Lecture Notes in Computer Science, vol 4287. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11925903_12
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DOI: https://doi.org/10.1007/11925903_12
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