Genomic scaffold filling revisited

DOI10.4230/LIPICS.CPM.2016.15MaRDI QIDQ5369550zbMATH OpenOpenAlexFDO

Authors Haitao Jiang, Chenglin Fan, Boting Yang, Farong Zhong, Daming Zhu, Binhai Zhu

Publication date 17 October 2017

Full work available at URL http://dx.doi.org/10.4230/LIPIcs.CPM.2016.15

zbMATH Keywords

approximation algorithmscomputational biologyFPT algorithmsNP-completeness

Mathematics Subject Classification ID

Computational difficulty of problems (lower bounds, completeness, difficulty of approximation, etc.) (68Q17) Approximation algorithms (68W25) Algorithms on strings (68W32) Genetics and epigenetics (92D10)

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Cited in

(13)

• On the solution bound of two-sided scaffold filling
• A new approximation algorithm for contig-based genomic scaffold filling
• New results about the linearization of scaffolds sharing repeated contigs
• Fixed-parameter algorithms for scaffold filling
• Gap filling as exact path length problem
• A polynomial time solution for permutation scaffold filling
• Filling Scaffolds with Gene Repetitions: Maximizing the Number of Adjacencies
• Fixed-parameter algorithms for scaffold filling
• Approximation and nonapproximability for the one-sided scaffold filling problem
• Genomic scaffold filling: a progress report
• The algorithm for the two-sided scaffold filling problem
• The floor is lava -- halving genomes with viaducts, piers and pontoons
• A 2.57-approximation algorithm for contig-based genomic scaffold filling

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