Patent ID: 8606553
Filing Date: 2013-12-10
Classification: C12N,G16B,G16C

Abstract:
1. A method performed in a computer of simulating a metabolic capability of an in silico strain of a microbe, comprising: obtaining a plurality of DNA sequences comprising most metabolic genes in a genome of the microbe to produce an in silico representation of a microbe; determining open reading frames of genes of unknown function in the microbe in said plurality of DNA sequences; assigning a potential function to proteins encoded by said open reading by determining the homology of said open reading frames to gene sequences encoding proteins of known function in a different organism; determining which of said open reading frames potentially correspond to metabolic genes by determining if the assigned function of said proteins is involved in cellular metabolism; determining substrates, products and stoichiometry of the reaction for each of the gene products of said metabolic genes having an assigned potential function; producing a genome specific stoichiometric matrix of said microbe produced by incorporating said substrates, products and stoichiometry into a stoichiometric matrix; determining a metabolic demand corresponding to a biomass composition of said microbe; calculating uptake rates of metabolites of said microbe; combining said metabolic demands and said uptake rates with said stoichiometric matrix to produce an in silico representation of said microbe; incorporating a general linear programming problem to produce an in silico strain of said microbe; performing a flux balance analysis on said in silico strain, and providing a visual output to a user of said analysis that simulates a metabolic capability of said strain predictive of said microbe's phenotype.