Using the longest run subsequence problem within homology-based scaffolding

Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related specie...

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Veröffentlicht in:	Algorithms for molecular biology Jg. 16; H. 1; S. 1 - 11
Hauptverfasser:	Schrinner, Sven, Goel, Manish, Wulfert, Michael, Spohr, Philipp, Schneeberger, Korbinian, Klau, Gunnar W.
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London BioMed Central 28.06.2021 Springer Nature B.V BMC
Schlagworte:	Algorithms Alignment Assembly Bioinformatics Biomedical and Life Sciences Cellular and Medical Topics Chromosomes Computational Biology/Bioinformatics Computer applications Genomes Homology Life Sciences Linear programming Longest subsequence Mutation Physiological Scaffolding Selected papers from WABI 2020 Source code String algorithm String algorithm Alignment Longest subsequence Assembly
ISSN:	1748-7188, 1748-7188
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Abstract	Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time.
AbstractList	Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time.Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time. Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time. Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time. Abstract Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time.
ArticleNumber	11
Author	Klau, Gunnar W. Wulfert, Michael Spohr, Philipp Schrinner, Sven Schneeberger, Korbinian Goel, Manish
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Cites_doi	10.1186/s13059-019-1911-0 10.1101/gr.214874.116 10.1093/bioinformatics/btaa253 10.1186/s13059-019-1829-6 10.1186/s13059-014-0573-1 10.1287/opre.32.6.1195 10.1186/s13059-017-1213-3 10.1038/35048692 10.1038/nbt.2727 10.1093/bioinformatics/bts480 10.1371/journal.pcbi.1005944 10.1101/gr.213652.116
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Snippet	Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based... Abstract Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based...
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SubjectTerms	Algorithms Alignment Assembly Bioinformatics Biomedical and Life Sciences Cellular and Medical Topics Chromosomes Computational Biology/Bioinformatics Computer applications Genomes Homology Life Sciences Linear programming Longest subsequence Mutation Physiological Scaffolding Selected papers from WABI 2020 Source code String algorithm
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Title	Using the longest run subsequence problem within homology-based scaffolding
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