Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/5283
Title: CAMPways: Constrained alignment framework for the comparative analysis of a pair of metabolic pathways
Authors: Abaka, Gamze
Bıyıkoğlu, Türker
Erten, Cesim
Keywords: Algorithms
Metabolic engineering
Metabolism
Metabolic pathways
Metabolic networks
Publisher: Oxford University Press
Source: Abaka, G., Bıyıkoğlu, T., and Erten, C. (2013). CAMPways: Constrained alignment framework for the comparative analysis of a pair of metabolic pathways. Bioinformatics, 29(13), i145-i153. doi.10.1093/bioinformatics/btt235
Abstract: Motivation: 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. © The Author 2013.
URI: http://doi.org/10.1093/bioinformatics/btt235
http://hdl.handle.net/11147/5283
ISSN: 1367-4803
1367-4803
Appears in Collections:Mathematics / Matematik
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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