2021
DOI: 10.48550/arxiv.2102.12822
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Algorithms and Complexity on Indexing Founder Graphs

Abstract: We introduce a compact pangenome representation based on an optimal segmentation concept that aims to reconstruct founder sequences from a multiple sequence alignment (MSA). Such founder sequences have the feature that each row of the MSA is a recombination of the founders. Several linear time dynamic programming algorithms have been previously devised to optimize segmentations that induce founder blocks that then can be concatenated into a set of founder sequences. All possible concatenation orders can be exp… Show more

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