Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/5283
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dc.contributor.authorAbaka, Gamze-
dc.contributor.authorBıyıkoğlu, Türker-
dc.contributor.authorErten, Cesim-
dc.date.accessioned2017-04-11T08:28:45Z
dc.date.available2017-04-11T08:28:45Z
dc.date.issued2013-07
dc.identifier.citationAbaka, 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/btt235en_US
dc.identifier.issn1367-4803
dc.identifier.issn1367-4803-
dc.identifier.urihttp://doi.org/10.1093/bioinformatics/btt235
dc.identifier.urihttp://hdl.handle.net/11147/5283
dc.description.abstractMotivation: 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.en_US
dc.description.sponsorshipTUBITAK (112E137); TÜBA GEBIP 2009 and ESF EUROCORES TUBITAK (210T173)en_US
dc.language.isoenen_US
dc.publisherOxford University Pressen_US
dc.relation.ispartofBioinformaticsen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectAlgorithmsen_US
dc.subjectMetabolic engineeringen_US
dc.subjectMetabolismen_US
dc.subjectMetabolic pathwaysen_US
dc.subjectMetabolic networksen_US
dc.titleCAMPways: Constrained alignment framework for the comparative analysis of a pair of metabolic pathwaysen_US
dc.typeArticleen_US
dc.institutionauthorBıyıkoğlu, Türker-
dc.departmentİzmir Institute of Technology. Mathematicsen_US
dc.identifier.volume29en_US
dc.identifier.issue13en_US
dc.identifier.startpagei145en_US
dc.identifier.endpagei153en_US
dc.identifier.wosWOS:000321746100017en_US
dc.identifier.scopus2-s2.0-84879975686en_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.identifier.doi10.1093/bioinformatics/btt235-
dc.identifier.pmid23812978en_US
dc.relation.doi10.1093/bioinformatics/btt235en_US
dc.coverage.doi10.1093/bioinformatics/btt235en_US
dc.identifier.wosqualityQ1-
dc.identifier.scopusqualityQ1-
item.openairetypeArticle-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.grantfulltextopen-
item.fulltextWith Fulltext-
item.languageiso639-1en-
item.cerifentitytypePublications-
crisitem.author.dept04.02. Department of Mathematics-
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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