title: Evolutionary algorithm for metabolic pathways synthesis.
abstract: Metabolic pathway building is an active field of research, necessary to understand and manipulate the metabolism of organisms. There are different approaches, mainly based on classical search methods, to find linear sequences of reactions linking two compounds. However, an important limitation of these methods is the exponential increase of search trees when a large number of compounds and reactions is considered. Besides, such models do not take into account all substrates for each reaction during the search, leading to solutions that lack biological feasibility in many cases. This work proposes a new evolutionary algorithm that allows searching not only linear, but also branched metabolic pathways, formed by feasible reactions that relate multiple compounds simultaneously. Tests performed using several sets of reactions show that this algorithm is able to find feasible linear and branched metabolic pathways.
authors.affiliation: Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina. Electronic address: mgerard@sinc.unl.edu.ar.
authors.forename: Matias F
authors.initials: MF
authors.lastname: Gerard
authors.affiliation: Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina. Electronic address: gstegmayer@sinc.unl.edu.ar.
authors.forename: Georgina
authors.initials: G
authors.lastname: Stegmayer
authors.affiliation: Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL/CONICET, Argentina. Electronic address: dmilone@sinc.unl.edu.ar.
authors.forename: Diego H
authors.initials: DH
authors.lastname: Milone
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000502:physiology*
keywords: De novo pathway building; Evolutionary algorithms; Reactions network; Search strategies; Sets of compounds