A hybrid algorithm for the DNA sequencing problem

DOI10.1016/J.DAM.2012.08.025MaRDI QIDQ406500zbMATH OpenOpenAlexFDO

Authors Marco Caserta, Stefan Voß

Publication date 8 September 2014

Published in Discrete Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.dam.2012.08.025

zbMATH Keywords

metaheuristicsinteger programmingDNA sequencingmatheuristicshealth care: bioinformatics

Mathematics Subject Classification ID

Approximation methods and heuristics in mathematical programming (90C59) Protein sequences, DNA sequences (92D20) Integer programming (90C10)

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Cites work

• scientific article; zbMATH DE number 5152600 (Why is no real title available?)
• scientific article; zbMATH DE number 2064417 (Why is no real title available?)
• A cross entropy-lagrangean hybrid algorithm for the multi-item capacitated lot-sizing problem with setup times
• A survey of very large-scale neighborhood search techniques
• A tutorial on the cross-entropy method
• Complexity of DNA sequencing by hybridization.
• DNA Sequencing by Hybridization via Genetic Search
• DNA sequencing-tabu and scatter search combined
• Dealing with repetitions in sequencing by hybridization
• Decremental state space relaxation strategies and initialization heuristics for solving the orienteering problem with time windows with dynamic programming
• Handbook of constraint programming.
• Hybrid genetic algorithm for DNA sequencing with errors
• Integer Programming Formulation of Traveling Salesman Problems
• Local branching
• Locating a cycle in a transportation or a telecommunications network
• Matheuristics
• POPMUSIC -- partial optimization metaheuristic under special intensification conditions
• Solving the Orienteering Problem through Branch-and-Cut
• Tabu search for DNA sequencing with false negatives and false positives
• The transform likelihood ratio method for rare event simulation with heavy tails

Cited in

(18)

• Algorithms for mixed-model sequencing with due date restrictions
• A hyper-heuristic approach to sequencing by hybridization of DNA sequences
• Combinatorial algorithms for DNA sequence assembly
• Optimization in Sanger sequencing
• Adaptive Iterated Local Search with Random Restarts for the Balanced Travelling Salesman Problem
• A Hybrid Genetic Algorithm for the DNA Fragment Assembly Problem
• Algorithms for testing that sets of DNA words concatenate without secondary structure
• scientific article; zbMATH DE number 2087017 (Why is no real title available?)
• Initialization of metaheuristics: comprehensive review, critical analysis, and research directions
• On the role of metaheuristic optimization in bioinformatics
• An ant colony optimization algorithm for DNA sequencing by hybridization
• scientific article; zbMATH DE number 5671091 (Why is no real title available?)
• DNA sequencing-tabu and scatter search combined
• Tabu search for DNA sequencing with false negatives and false positives
• Balanced VCG mechanisms for sequencing problems
• Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms
• Hybrid genetic algorithm for DNA sequencing with errors
• Modeling and optimization of genetic screens via RNA interference and FACS

Describes a project that uses

Uses Software

• Bioconductor
• POPMUSIC

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