Maximum-scoring path sets on pangenome graphs of constant treewidth

We generalize a problem of finding maximum-scoring segment sets, previously studied by Csűrös (IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004, 1, 139–150), from sequences to graphs. Namely, given a vertex-weighted graph G and a non-negative startup penalty c , we can find a...

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Bibliographic Details
Published in:Frontiers in bioinformatics Vol. 4; p. 1391086
Main Authors: Brejová, Broňa, Gagie, Travis, Herencsárová, Eva, Vinař, Tomáš
Format: Journal Article
Language:English
Published: Switzerland Frontiers Media S.A 01.07.2024
Subjects:
Bioinformatics
dynamic programming
elastic degenerate strings
pangenomics
treewidth
weighted paths
dynamic programming
elastic degenerate strings
weighted paths
pangenomics
treewidth
ISSN:2673-7647, 2673-7647
Online Access:Get full text
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Summary:We generalize a problem of finding maximum-scoring segment sets, previously studied by Csűrös (IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004, 1, 139–150), from sequences to graphs. Namely, given a vertex-weighted graph G and a non-negative startup penalty c , we can find a set of vertex-disjoint paths in G with maximum total score when each path’s score is its vertices’ total weight minus c . We call this new problem maximum-scoring path sets (MSPS). We present an algorithm that has a linear-time complexity for graphs with a constant treewidth. Generalization from sequences to graphs allows the algorithm to be used on pangenome graphs representing several related genomes and can be seen as a common abstraction for several biological problems on pangenomes, including searching for CpG islands, ChIP-seq data analysis, analysis of region enrichment for functional elements, or simple chaining problems.
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Manuel Caceres, Aalto University, Finland
Edited by: Cinzia Pizzi, University of Padua, Italy
Reviewed by: Gianluca Della Vedova, University of Milano-Bicocca, Italy
ISSN:2673-7647
2673-7647
DOI:10.3389/fbinf.2024.1391086