RPS:a Software Tool to Recommend Host Organisms and Exogenous Enzymes for Designing Synthetic Metabolic Pathways
Selecting host organisms for synthetic metabolic pathways and determining exogenous enzymes for exogenous reactions in synthetic metabolic pathways are two challenges of synthetic biology and metabolic engineering.Due to thousands of microorganisms and biosynthetic reactions existing in nature,it is expensive and time-consuming to identify such goals only via biological experiments.This paper develops a novel biological reasoning software called RPS(recommend metabolic pathway's species)for synthetic metabolic path-way design.For synthetic metabolic pathways,the RPS software tool suggests suitable host organisms based on the ratios of competing endogenous reactions and the number of dead-end metabolites,and identifies appropriate exogenous enzymes of exogenous reactions in host organism via phylogenetic distance and reaction kinetics of enzymes.These pathway-centered features distinguish the RPS software from the existing host-centered synthetic metabolic pathway design tools and enable researchers to assess the design of their synthetic metabolic pathways in a different view.Experimental results show that the RPS software tool can accurately identify potential host or-ganisms for synthetic metabolic pathways and discover suitable exogenous enzymes for exogenous reactions in synthetic metabolic path-ways.Users can execute the RPS software online via https://biolab.gxu.edu.cn/RPS.
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