RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Annealed Embeddings of Communication Patterns in an Interconnection Cached Network
IEEE Transactions on Parallel and Distributed Systems
The restriction mapping problem revisited
Journal of Computer and System Sciences - Computational biology 2002
The Enhanced Double Digest Problem for DNA Physical Mapping
SWAT '00 Proceedings of the 7th Scandinavian Workshop on Algorithm Theory
On the complexity of the DNA simplified partial digest problem
CATS '06 Proceedings of the 12th Computing: The Australasian Theroy Symposium - Volume 51
Partial digest is hard to solve for erroneous input data
Theoretical Computer Science
International Journal of Bioinformatics Research and Applications
The Double Digest Problem: finding all solutions
International Journal of Bioinformatics Research and Applications
Reconstructing Numbers from Pairwise Function Values
ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
Double digest revisited: complexity and approximability in the presence of noisy data
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Genetic algorithm for double digest problem
PReMI'05 Proceedings of the First international conference on Pattern Recognition and Machine Intelligence
Paper: A constraint logic programming framework for constructing DNA restriction maps
Artificial Intelligence in Medicine
On the complexity of the DNA simplified partial digest problem
CATS '06 Proceedings of the Twelfth Computing: The Australasian Theory Symposium - Volume 51
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The multiple digest mapping problem arising in molecular biology can be stated roughly as follows. A linear or circular segment of DNA is cut at all occurrences of a specific short pattern by restriction enzymes. By using restriction enzymes singly and in combination it is required to construct a map showing the location of cleavage sites. In this paper we first consider the efficacy of a simulated annealing algorithm towards the solution to the multiple digest problem. Second, the double digest problem, the simplest version of the multiple digest problem with only two restriction enzymes used, is shown to admit an exponentially increasing number of solutions as a function of the length of the segment under a particular probability model. Next, the double digest problem is shown to lie in the class of NP complete problems which are conjectured to have no polynomial time solution. Last, the construction of circular maps is considered and the problem of measurement error is discussed.