Algorithmic approaches for the single individual haplotyping problem

DOI10.1051/RO/2015037MaRDI QIDQ2805490zbMATH OpenOpenAlexFDO

Authors Giuseppe Lancia

Publication date 11 May 2016

Published in RAIRO. Operations Research (Search for Journal in Brave)

Full work available at URL https://semanticscholar.org/paper/bad61d7934f8ecf6e4c5e5752bba499aa8fbf1cd

zbMATH Keywords

minimum fragmenthaplotyping problem

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Protein sequences, DNA sequences (92D20) Software, source code, etc. for problems pertaining to biology (92-04)

Recommendations

• Polynomial and APX-hard cases of the individual haplotyping problem
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• The haplotyping problem: an overview of computational models and solutions
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Cites work

• scientific article; zbMATH DE number 3639144 (Why is no real title available?)
• scientific article; zbMATH DE number 1945152 (Why is no real title available?)
• scientific article; zbMATH DE number 1877046 (Why is no real title available?)
• An improved (and practical) parameterized algorithm for the individual haplotyping problem MFR with mate-pairs
• Enhanced evolutionary and heuristic algorithms for haplotype reconstruction problem using minimum error correction model
• Haplotype assembly from aligned weighted SNP fragments
• Opportunities for combinatorial optimization in computational biology
• Polynomial and APX-hard cases of the individual haplotyping problem
• Testing for the consecutive ones property, interval graphs, and graph planarity using PQ-tree algorithms
• The complexity of the single individual SNP haplotyping problem

Cited in

(5)

• On the Approximability of Some Haplotyping Problems
• Recent advances in operations research in computational biology, bioinformatics and medicine
• Self-organizing map approaches for the haplotype assembly problem
• Computational Methods for SNPs and Haplotype Inference
• A guided tour to computational haplotyping

Describes a project that uses

Uses Software

• ReFHap
• ReHap
• HapCUT
• SpeedHap

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