Abstract:Indexing labeled graphs for pattern matching is a central challenge of pangenomics. Equi et al. (Algorithmica, 2022) developed the Elastic Founder Graph (EFG) representing an alignment of m sequences of length n, drawn from alphabet Σ plus the special gap character: the paths spell the original sequences or their recombination. By enforcing the semi-repeat-free property, the EFG admits a polynomial-space index for linear-time pattern matching, breaking through the conditional lower bounds on indexing labeled … Show more
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