An integer programming approach to DNA sequence assembly

DOI10.1016/J.COMPBIOLCHEM.2011.06.001zbMATH Open1226.92019OpenAlexW1979646490WikidataQ44483592 ScholiaQ44483592MaRDI QIDQ647296FDOQ647296

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

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zbMATH Keywords

global optimizationinteger programmingDNA sequencingalternative solutionsshort reads assembly

Mathematics Subject Classification ID

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

Cites Work

• Title not available (Why is that?)
• Complexity of DNA sequencing by hybridization.
• Title not available (Why is that?)
• Euler circuits and DNA sequencing by hybridization
• An ant colony optimization algorithm for DNA sequencing by hybridization
• An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors
• Mathematical programming in computational biology: an annotated bibliography
• Sequencing by hybridization with errors: handling longer sequences
• Integer Linear Programming in Computational Biology
• Restricting SBH ambiguity via restriction enzymes

Cited In (10)

• 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
• Title not available (Why is that?)
• Balanced VCG mechanisms for sequencing problems
• DNA fragments assembly programs: A comparative study
• Combinatorial algorithms for DNA sequence assembly
• DNA fragment assembly using a grid-based genetic algorithm
• Title not available (Why is that?)
• Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms
• An Eulerian path approach to DNA fragment assembly

Uses Software

• CPLEX

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