The simplified partial digest problem: Enumerative and dynamic programming algorithms

Citation

Blazewicz J, Burke E, Kasprzak M, Kovalev A & Kovalyov MY (2007) The simplified partial digest problem: Enumerative and dynamic programming algorithms. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4 (4), pp. 668-680. https://doi.org/10.1109/TCBB.2007.1060

Abstract
We study the simplified partial digest problem (SPDP), which is a mathematical model for a new simplified partial digest method of genome mapping. This method is easy for laboratory implementation and robust with respect to the experimental errors. SPDP is NP-hard in the strong sense. We present an O(n2n) time enumerative algorithm (ENUM) and an O(n2q) time dynamic programming algorithm for the error-free SPDP, where n is the number of restriction sites and q is the number of distinct intersite distances. We also give examples of the problem in which there are 2n+2/3 -1 noncongruent solutions. These examples partially answer a question recently posed in the literature about the number of solutions of SPDP. We adapt our ENUM for handling SPDP with imprecise input data. Finally, we describe and discuss the results of the computer experiments with our algorithms.

Keywords
DNA; biochemistry; biology computing; combinatorial mathematics; computational complexity; dynamic programming; genetics; molecular biophysics

Journal
IEEE/ACM Transactions on Computational Biology and Bioinformatics: Volume 4, Issue 4