ArticleFrontiers in bioinformatics2024
Pangenome comparison via ED strings.
Article in Frontiers in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Pattern matching with Elastic-Degenerate strings and Elastic-Founder graphs.Algorithms for molecular biology : AMB · 2026Article
- Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs.Bioinformatics (Oxford, England) · 2025Article
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Authors and funding
7 authors.
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Abstract
Introduction: An elastic-degenerate (ED) string is a sequence of sets of strings. It can also be seen as a directed acyclic graph whose edges are labeled by strings. The notion of ED strings was introduced as a simple alternative to variation and sequence graphs for representing a pangenome, that is, a collection of genomic sequences to be analyzed jointly or to be used as a reference. Methods: In this study, we define notions of Results: We also implemented our methods as a software tool for pangenome comparison and evaluated their efficiency and effectiveness using both synthetic and real datasets. Discussion: As for efficiency, we compare the runtime of the intersection graph method against the classic product automaton construction showing that the intersection graph is faster by up to one order of magnitude. For showing effectiveness, we used real SARS-CoV-2 datasets and our matching statistics similarity measure to reproduce a well-established clade classification of SARS-CoV-2, thus demonstrating that the classification obtained by our method is in accordance with the existing one.
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