Campways: Constrained Alignment Framework for the Comparative Analysis of a Pair of Metabolic Pathways
dc.contributor.author | Abaka, Gamze | |
dc.contributor.author | Biyikoglu, Turker | |
dc.contributor.author | Erten, Cesim | |
dc.date.accessioned | 2019-06-27T08:03:30Z | |
dc.date.available | 2019-06-27T08:03:30Z | |
dc.date.issued | 2013 | |
dc.department | Fakülteler, Mühendislik ve Doğa Bilimleri Fakültesi, Bilgisayar Mühendisliği Bölümü | en_US |
dc.description.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. | en_US] |
dc.identifier.citation | 14 | |
dc.identifier.doi | 10.1093/bioinformatics/btt235 | en_US |
dc.identifier.endpage | 153 | |
dc.identifier.issn | 1367-4803 | en_US |
dc.identifier.issn | 1460-2059 | en_US |
dc.identifier.issn | 1367-4803 | |
dc.identifier.issn | 1460-2059 | |
dc.identifier.issue | 13 | |
dc.identifier.pmid | 23812978 | en_US |
dc.identifier.scopus | 2-s2.0-84879975686 | en_US |
dc.identifier.startpage | 145 | en_US |
dc.identifier.uri | https://hdl.handle.net/20.500.12469/800 | |
dc.identifier.uri | https://doi.org/10.1093/bioinformatics/btt235 | |
dc.identifier.volume | 29 | en_US |
dc.identifier.wos | WOS:000321746100017 | en_US |
dc.identifier.wosquality | Q1 | |
dc.institutionauthor | Abaka, Gamze | en_US |
dc.institutionauthor | Erten, Cesim | |
dc.language.iso | en | en_US |
dc.publisher | Oxford University Press | en_US |
dc.relation.journal | Bioinformatics | en_US |
dc.relation.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | en_US |
dc.rights | info:eu-repo/semantics/openAccess | en_US |
dc.title | Campways: Constrained Alignment Framework for the Comparative Analysis of a Pair of Metabolic Pathways | en_US |
dc.type | Article | en_US |
dspace.entity.type | Publication | |
relation.isAuthorOfPublication | ba94d962-58f9-4c10-bdc8-667be0ec3b67 | |
relation.isAuthorOfPublication.latestForDiscovery | ba94d962-58f9-4c10-bdc8-667be0ec3b67 |
Files
Original bundle
1 - 1 of 1
Loading...
- Name:
- CAMPways constrained alignment framework for the comparative analysis of a pair of metabolic pathways.pdf
- Size:
- 414.1 KB
- Format:
- Adobe Portable Document Format
- Description: