AUTHOR=Brejová Broňa , Gagie Travis , Herencsárová Eva , Vinař Tomáš 

TITLE=Maximum-scoring path sets on pangenome graphs of constant treewidth

JOURNAL=Frontiers in Bioinformatics

VOLUME=4

YEAR=2024

URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1391086

DOI=10.3389/fbinf.2024.1391086

ISSN=2673-7647

ABSTRACT=<p>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 <italic>G</italic> and a non-negative startup penalty <italic>c</italic>, we can find a set of vertex-disjoint paths in <italic>G</italic> with maximum total score when each path’s score is its vertices’ total weight minus <italic>c</italic>. We call this new problem <italic>maximum-scoring path sets</italic> (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.</p>