Genomic scaffold filling: a progress report

DOI10.1007/978-3-319-39817-4_2MaRDI QIDQ4632164zbMATH OpenOpenAlexFDO

Authors Binhai Zhu

Publication date 26 April 2019

Published in Frontiers in Algorithmics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-319-39817-4_2

Mathematics Subject Classification ID

Algorithms on strings (68W32) Computational methods for problems pertaining to biology (92-08) Genetics and epigenetics (92D10)

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Cites work

• A 1.5-approximation algorithm for two-sided scaffold filling
• A polynomial time solution for permutation scaffold filling
• A retrospective on genomic preprocessing for comparative genomics
• An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies
• Approximation and nonapproximability for the one-sided scaffold filling problem
• Color-coding
• Filling Scaffolds with Gene Repetitions: Maximizing the Number of Adjacencies
• Fixed-parameter algorithms for scaffold filling
• Genomic scaffold filling revisited
• scientific article; zbMATH DE number 1507224 (Why is no real title available?)
• scientific article; zbMATH DE number 2119725 (Why is no real title available?)
• scientific article; zbMATH DE number 2234775 (Why is no real title available?)
• Non-breaking Similarity of Genomes with Gene Repetitions
• On Syntactic versus Computational Views of Approximability
• On the Approximability of Comparing Genomes with Duplicates
• On the approximability of the exemplar adjacency number problem for genomes with gene repetitions
• On the inapproximability of the exemplar conserved interval distance problem of genomes
• Parameterized complexity of Vertex Cover variants
• Parametrized complexity theory.
• The Approximability of the Exemplar Breakpoint Distance Problem
• The Exemplar Breakpoint Distance for Non-trivial Genomes Cannot Be Approximated

Cited in

(8)

• A new approximation algorithm for contig-based genomic scaffold filling
• Comparing incomplete sequences via longest common subsequence
• 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
• A retrospective on genomic preprocessing for comparative genomics
• Genomic scaffold filling revisited
• The floor is lava -- halving genomes with viaducts, piers and pontoons

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