Evolutionary algorithm for metabolic pathways synthesis

M. GERARD, G. STEGMAYER, D.H. MILONE

Buenos Aires

Simposio; ASAI 2016; 2016

SADIO

Several methods to automatically search for metabolic pathways among com-pounds have been developed in last years. They are mainly based on classicalsearch algorithms, such as breadth-first and depth-first search, and the A* al-gorithm. They first model data as an appropiate graph, and then perform thesearch of a pathway between compounds. Although they have served as a firstattempt to address the problem, these methods have at least one of the followinglimitations: i) they do not consider all the substrates for the reactions (feasibil-ity of reactions is not guaranteed); ii) they cannot model and build branchedmetabolic pathways; iii) they only search pathways between two compounds;iv) previously synthesized compounds in the reactions chain are not taken intoaccount to select a new reaction (just the last one). Frequently, it leads to findsolutions without biological sense. We propose a new algorithm based on evolutionary computation for searching branched metabolic pathways, that links simultaneously several compounds through feasible reactions. This proposal, named evolutionary metabolicsynthesizer (EvoMS), uses the concept of expanded set of compounds (ESC) tomodel metabolic pathways.