Abaka, GamzeBiyikoglu, TurkerErten, Cesim2019-06-272019-06-272013141367-48031460-20591367-48031460-2059https://hdl.handle.net/20.500.12469/800https://doi.org/10.1093/bioinformatics/btt235Motivation: Given a pair of metabolic pathways an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction drug design and overall may enhance our understanding of cellular metabolism. Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database we demonstrate that when compared with a state-of-the-art alternative the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms.eninfo:eu-repo/semantics/openAccessArticle1451531329WOS:00032174610001710.1093/bioinformatics/btt2352-s2.0-84879975686Q1N/A23812978