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Global alignment of metabolic pathways and protein-protein interaction networks
(Kadir Has Üniversitesi, 2014) Erten, Cesim; Erten, Cesim
Metabolic pathways and protein interaction networks are essential at almost every function for living organisms. Simply, while reactions produce life energy within cells, protein interaction networks provide biological functions. Also, abnormal reactions or interactions cause various disorders. Thus, in bioinformatics, most of the studies are based on these networks in order to find hopeful results for these disorders and biological challenges. Solving alignment problem is one of these studies such that it tries to find similar reactions, proteins or functions. In this thesis, we focus on that problem within both metabolic pathways and protein interaction networks. Firstly, we propose a constrained alignment algorithm, CAMPways, for one-to-many alignment of metabolic pathways and we extend the framework, CAPPI, for one-to-one protein interaction network alignment with necessary changes. Afterwards, we provide the computational intractability of the problem and finally we compare our algorithm with different algorithms on actual metabolic pathways and protein interaction networks.