Mapping DNA by stochastic relaxation
Advances in Applied Mathematics
Reconstructing sets from interpoint distances (extended abstract)
SCG '90 Proceedings of the sixth annual symposium on Computational geometry
Data structures and algorithm analysis in C++
Data structures and algorithm analysis in C++
Regular Article: A Lower Bound on the Number of Solutions to the Probed Partial Digest Problem
Advances in Applied Mathematics
Algorithms for optical mapping
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
De Novo peptide sequencing via tandem mass spectrometry: a graph-theoretical approach
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
On the turnpike problem
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
Reconstructing Numbers from Pairwise Function Values
ISAAC '09 Proceedings of the 20th International Symposium on Algorithms and Computation
On the complexity of the DNA simplified partial digest problem
CATS '06 Proceedings of the Twelfth Computing: The Australasian Theory Symposium - Volume 51
Genetic algorithm solution for partial digest problem
International Journal of Bioinformatics Research and Applications
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In computational molecular biology, the aim of restriction mapping is to locate the restriction sites of a given enzyme on a DNA molecule. Double digest and partial digest are two well-studied techniques for restriction mapping. While double digest is NP-complete, there is no known polynomial-time algorithm for partial digest. Another disadvantage of the above techniques is that there can be multiple solutions for reconstruction.In this paper, we study a simple technique called labeled partial digest for restriction mapping. We give a fast polynomial time (O(n2 log n) worst-case) algorithm for finding all the n sites of a DNA molecule using this technique. An important advantage of the algorithm is the unique reconstruction of the DNA molecule from the digest. The technique is also robust in handling errors in fragment lengths which arises in the laboratory. We give a robust O(n4) worst-case algorithm that can provably tolerate an absolute error of O(δ/n) (where δ is the minimum inter-site distance), while giving a unique reconstruction. We test our theoretical results by simulating the performance of the algorithm on a real DNA molecule.Motivated by the similarity to the labeled partial digest problem, we address a related problem of interest--the de novo peptide sequencing problem (ACM-SIAM Symposium on Discrete Algorithms (SODA), 2000, pp. 389-398), which arises in the reconstruction of the peptide sequence of a protein molecule. We give a simple and efficient algorithm for the problem without using dynamic programming. The algorithm runs in time O(k log k), where k is the number of ions and is an improvement over the algorithm in Chen et al.