An integer programming approach to DNA sequence assembly

DOI10.1016/J.COMPBIOLCHEM.2011.06.001MaRDI QIDQ647296zbMATH OpenOpenAlexWikidataFDO

Authors Youngjung Chang, Nikolaos V. Sahinidis

Publication date 22 November 2011

Published in Computational Biology and Chemistry (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.compbiolchem.2011.06.001

zbMATH Keywords

global optimizationinteger programmingDNA sequencingalternative solutionsshort reads assembly

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Biomechanics (92C10)

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Cites work

• scientific article; zbMATH DE number 193411 (Why is no real title available?)
• scientific article; zbMATH DE number 1557065 (Why is no real title available?)
• An ant colony optimization algorithm for DNA sequencing by hybridization
• An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors
• Complexity of DNA sequencing by hybridization.
• Euler circuits and DNA sequencing by hybridization
• Integer Linear Programming in Computational Biology
• Mathematical programming in computational biology: an annotated bibliography
• Restricting SBH ambiguity via restriction enzymes
• Sequencing by hybridization with errors: handling longer sequences

Cited in

(12)

• Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms
• An Eulerian path approach to DNA fragment assembly
• A polynomial time equivalence between DNA sequencing and the exact perfect matching problem
• The matrix iteration algorithm solving an enumeration problem on bacterial complete genomes
• scientific article; zbMATH DE number 2013796 (Why is no real title available?)
• DNA sequence assembly involving an acyclic graph model
• Balanced VCG mechanisms for sequencing problems
• DNA fragments assembly programs: A comparative study
• Combinatorial algorithms for DNA sequence assembly
• DNA sequence assembly of \textit{Paenibacillus Shenyangensis}
• DNA fragment assembly using a grid-based genetic algorithm
• scientific article; zbMATH DE number 2130802 (Why is no real title available?)

Describes a project that uses

Uses Software

• CPLEX

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