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The Enhanced Double Digest Problem for DNA Physical Mapping
[article]
2001
arXiv
pre-print
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The double digest problem is a common NP-hard approach to constructing physical maps of DNA sequences. This paper presents a new approach called the enhanced double digest problem. ...
Although this new problem is also NP-hard, it can be solved in linear time in certain theoretically interesting cases. ...
Then, all the elements in C are different and we can solve the enhanced double digest problem using the algorithm Enhanced-Double-Digest in Section 3.2. ...
arXiv:cs/0102010v1
fatcat:niqexd6q3vdbdmu5jqvrayyyiy
DDmap: a MATLAB package for the double digest problem using multiple genetic operators
2019
BMC Bioinformatics
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In computational biology, the physical mapping of DNA is a key problem. We know that the double digest problem (DDP) is NP-complete. ...
Based on our simulations on 1000 random DDP instances by using DDmap, we find that the maximum length of the combining fragments has observable effects towards genetic algorithms for solving the DDP problem ...
Acknowledgements We thank the anonymous reviewers for giving us valuable suggestions.
Availability of data and materials DDmap is open source and available at https://github.com/wanglc2012/DDmap. ...
doi:10.1186/s12859-019-2862-x
fatcat:3mkfiqjwwbcf3dtcftgsucga5e
Double Digest Revisited: Complexity and Approximability in the Presence of Noisy Data
[chapter]
2003
Lecture Notes in Computer Science
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We revisit the double digest problem, which occurs in sequencing of large DNA strings and consists of reconstructing the relative positions of cut sites from two different enzymes: we rst show that double ...
making it impossible to guarantee any approximation ratio at all. ...
NP-hardness of Finding Feasible Solutions for Optimization Variations of Disjoint Double Digest In this section, we show that all Double Digest optimization variations in which we disallow coincidences ...
doi:10.1007/3-540-45071-8_52
fatcat:mwhnq5dpu5aufnl5rszpok5ofm
Genetic Algorithm for Double Digest Problem
[chapter]
2005
Lecture Notes in Computer Science
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The strongly NP-complete Double Digest Problem (DDP) for physical mapping of DNA, is now used for efficient genotyping. An instance of DDP has multiple distinct solutions. ...
Existing methods produce a single solution, and are slow for large instances. We employ a type of equivalence among the distinct solutions to obtain almost all of them. ...
Problem Formulation The combinatorial description of Double Digest Problem (DDP) is as follows [12] : let A = {a i : 1 ≤ i ≤ m}, B = {b i : 1 ≤ i ≤ n} and A + B = {d i : 1 ≤ i ≤ l} m i=1 a i = n i=1 ...
doi:10.1007/11590316_99
fatcat:trlvwojfwbhxxetdjuu2i26zju
A Randomized, Double-blinded Comparison of Phenylephrine and Ephedrine Infusion Combinations to Maintain Blood Pressure During Spinal Anesthesia for Cesarean Delivery: The Effects on Fetal Acid-Base Status and Hemodynamic Control
2009
Obstetric Anesthesia Digest
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RESULTS: As the proportion of phenylephrine decreased and proportion of ephedrine increased among the groups, the following significant trends were detected: the incidences of hypotension and nausea/vomiting ...
However, the effect of varying the proportion of vasopressors in such combinations has not been reported. ...
ACKNOWLEDGMENTS The authors thank the midwives of the Labor Ward, Prince of Wales Hospital, Shatin, Hong Kong, China for their assistance and co-operation. ...
doi:10.1097/01.aoa.0000358410.78531.07
fatcat:mmxlmeyqeffini3gsrzb2turay
Multiple solutions of DNA restriction mapping problems
1991
Advances in Applied Mathematics
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In this paper we define a hierarchy of equivalence relations on the set of all solutions to the mapping problem and study the combinatorics and characterization of the equivalence classes. o 1991 Academic ...
However, it is also known that under a simple model of randomness the number of solutions to the mapping problem increases exponentially with the length of the DNA molecule. ...
First of all, the solution to a particular double digest problem is usually far from unique. ...
doi:10.1016/0196-8858(91)90028-h
fatcat:5hynwbjcbnf6nazo2f5jrys6k4
The restriction mapping problem revisited
2002
Journal of computer and system sciences (Print)
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We give a fast polynomial time (Oðn 2 log nÞ worst-case) algorithm for finding all the n sites of a DNA molecule using this technique. ...
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. ...
Acknowledgments We are grateful to an anonymous referee for the excellent suggestion of applying our technique to the peptide sequencing problem and for pointing out useful references. ...
doi:10.1016/s0022-0000(02)00008-9
fatcat:sbsmbdoa3jcpzk74eit62n4xtm
Genetic algorithm solution for double digest problem
2012
Bioinformation
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The strongly NP-Hard Double Digest Problem, for reconstructing the physical map of DNA sequence, in now using for efficient genotyping. ...
Most of the existing methods are inefficient in tackling large instances due to the large search space for the problem which grows as a factorial function ISSN 0973-2063 (online) 0973-8894 (print) Bioinformation ...
Conclusion: A novel genetic algorithm is designed for solving double digest problem. ...
doi:10.6026/97320630008453
pmid:22715298
pmcid:PMC3374354
fatcat:tqs3edk6hzbehbfirsjtcngs6i
Quantum Inspired Genetic Algorithm for Double Digest Problem
2020
IEEE Access
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The double digest problem (DDP) is a fundamental problem in bioinformatics, and it has been proven to be an NP-hard problem. ...
The solution of the DDP is a permutation, selected by the QIGA, of all the DNA fragments. ...
In Fig. 3(b) , only SK05 cannot find the exact solution of the double digest problem. ...
doi:10.1109/access.2020.2988117
fatcat:fptmcicewffnfa3g5qvfcvqdhm
PROBLEM DEPARTMENT
1933
School Science and Mathematics
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(a) Asum of X dollars, invested at X per cent, compounded annually, doubles itself in X years. Find X, other than 0. ...
All readers are invited to propose problems and to solve problems here pro
posed. ...
doi:10.1111/j.1949-8594.1933.tb14158.x
fatcat:p53lhmisqfgbhk3tvojem7f754
PROBLEM DEPARTMENT
1934
School Science and Mathematics
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All readers are invited to propose problems and to solve problems here pro- posed. Drawings to illustrate the problems should be well done in India ink. ...
Each solution, or proposed problem, sent to the Editor should have the author’s name intro- ducing the problem or solution as on the following pages. ...
doi:10.1111/j.1949-8594.1934.tb09781.x
fatcat:7wymc4vojjdvtc3rj23dyahuo4
Solving large double digestion problems for DNA restriction mapping by using branch-and-bound integer linear programming
2008
International Journal of Bioinformatics Research and Applications
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The double digestion problem is to find the orders for a and b, given c as the result of the sequence being digested by A and B combined. ...
The double digestion problem for DNA restriction mapping has been proved to be NPcomplete, and is intractable if the numbers of the DNA fragments generated by the two restriction enzymes are large. ...
Another issue is the multiple solutions to the mixed-integer programs and hence the double digestion problem. ...
doi:10.1504/ijbra.2008.021173
pmid:19008180
fatcat:yavfudk5endq5kppwdyxktw6eu
On the approximability of the Simplified Partial Digest Problem
2009
Discrete Applied Mathematics
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In this paper, we analyse the computational complexity of an optimization version of the Simplified Partial Digest Problem (SPDP), which is a mathematical model for DNA mapping based on the results of ...
This implies that the problem of maximizing the number of correct elements of the DNA map in the error-free simplified partial digest experiment is pseudopolynomially non-approximable with the approximation ...
Acknowledgments This work was partially supported by the Polish Ministry of Science grant N519 314635 and the Marie Curie BIOPTRAIN fellowship of Mr. A. Kovalev. ...
doi:10.1016/j.dam.2009.04.017
fatcat:xvyuahgqzrecnam2gpygsdjkaa
Advanced Problems and Solutions
1960
The American mathematical monthly
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ADVANCED PROBLEMS AND SOLUTIONS
EpITED BY E. P. STaRKE, Rutgers, The State University
Send all communications concerning Advanced Problems and Solutions to E. P. ...
Starke, Rutgers, The State University, New Brunswick, New Jersey. All manuscripts should be type- written with double spacing and margins at least one inch wide. ...
doi:10.1080/00029890.1960.11989452
fatcat:i6hml3xthbgbdoqyho3wjy2k2q
DNA-Based Computing of Strategic Assignment Problems
2011
Physical Review Letters
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solving the same problem. ...
In this Letter, a new approach dealing with strategic assignment problems is proposed based on manipulating DNA strands, which is believed to be better than the conventional silicon-based computing in ...
-The following DNA-based algorithm is designed to solve the strategic assignment problem: Step 1: Generate all possible solution paths through the graph. ...
doi:10.1103/physrevlett.106.188702
pmid:21635133
fatcat:p3swbo3jhzb23f6f5tmiakvjra
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