Co-linear chaining with overlaps and gap costs

DOI10.1007/978-3-031-04749-7_15zbMath1497.92185OpenAlexW4285217451MaRDI QIDQ2170153

Daniel Gibney, Chirag Jain, Sharma V. Thankachan

Publication date: 30 August 2022

Full work available at URL: https://doi.org/10.1007/978-3-031-04749-7_15

zbMATH Keywords

alignmentedit distanceco-linear chaining

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Related Items (1)

Sequence to graph alignment using gap-sensitive co-linear chaining

Uses Software

• AVID
• Minimap2
• essaMEM
• Edlib
• Winnowing
• lra
• CoCoNUT
• MUMmer4

Cites Work

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• A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences
• Chaining algorithms for multiple genome comparison
• Edit Distance Cannot Be Computed in Strongly Subquadratic Time (unless SETH is false)
• A fast bit-vector algorithm for approximate string matching based on dynamic programming
• Algorithms for approximate string matching
• Sparse dynamic programming I
• Sparse dynamic programming II
• Sparse Dynamic Programming on DAGs with Small Width
• The Fine-Grained Complexity of Median and Center String Problems Under Edit Distance

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