Computational graph pangenomics: a tutorial on data structures and their applications

DOI10.1007/S11047-022-09882-6MaRDI QIDQ6155034zbMATH OpenOpenAlexFDO

Authors Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén

Publication date 16 February 2024

Published in Natural Computing (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.1007/s11047-022-09882-6

Mathematics Subject Classification ID

Data structures (68P05) Genetics and epigenetics (92D10)

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Cited in

(11)

• Can formal languages help pangenomics to represent and analyze multiple genomes?
• Sequence to graph alignment using gap-sensitive co-linear chaining
• From de Bruijn graphs to variation graphs -- relationships between pangenome models
• Complexity results and algorithms for representing paths in digraphs
• AlfaPang: alignment free algorithm for pangenome graph construction
• A unifying taxonomy of pattern matching in degenerate strings and founder graphs
• Fast pattern matching with epsilon transitions
• A Myhill-Nerode theorem for generalized automata, with applications to pattern matching and compression
• Elastic-degenerate string comparison
• Representing paths in digraphs
• Fast pattern matching with epsilon transitions

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