Reconstruction Of Microbial Metabolic Pathways By Computers And Construction Of Web Server

To know the biochemical phenomemon in organisms, the reconstruction of metabolic pathways by computers has been an important part in the bioinformatics area. The physiological pathways in organisms are only reconstructed by many researchers, who have not considered the production of target compound. The work of this paper was done based on the reconstruction of metabolic pathways with high production of target compound.Firstly, biological data downloaded from the KEGG web was pretreated to get rid of the common compounds and small molecules and then the reaction pairs were obtained to construct reaction matrix. Secondly, the weighting function, based on the influencing factors of production of target compound, was designed. These influencing factors including stoichiometric coefficient of reaction pair, connectivity of compound and the reaction reversible coefficient were recorded in literatures. The breadth first search approach was used to search metabolic pathways and the weighting function was used to calculate the value of these metabolic pathways as the production of target compound produced by unit initial compound. Finally, the web server searching microbial metabolic pathways was built with the PHP, Apache and MySQL technologies. This web server consists of six main modules, namely Single organism search, Comparative search, Virtual organism search, Constraint condition search, Compound structure similarity search and Protein-protein interaction analysis.This paper constructed many theoretical high production pathways, which provide data support for understanding the biochemical phenomemons in organisms. They can be led in a host to synthetize industrial metabolites under a proper condition.