{"doi":"10.3389/fbinf.2024.1391086","title":"Maximum-scoring path sets on pangenome graphs of constant treewidth","abstract":"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.","journal":"Frontiers in Bioinformatics","year":2024,"id":500330,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9361,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":662070,"name":"Travis Gagie","orcid":"0000-0003-3689-327X","position":1,"is_corresponding":false},{"id":1349985,"name":"Eva Herencsárová","orcid":null,"position":2,"is_corresponding":false},{"id":992788,"name":"Tomáš Vinař","orcid":"0000-0003-3898-3447","position":3,"is_corresponding":false},{"id":992789,"name":"Broňa Brejová","orcid":"0000-0002-9483-1766","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":null,"created_at":"2026-07-19T02:10:08.435215Z","pmid":"39011297","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}