Methods for identifying drug targets based on genomic sequence data
0 Assignments
0 Petitions
Accused Products
Abstract
This invention provides a computational approach to identifying potential antibacterial drug targets based on a genomic sequence and its annotation. Starting from a fully sequenced genome, open reading frame assignments are made which determine the metabolic genotype for the organism. The metabolic genotype, and more specifically its stoichiometric matrix, are analyzed using flux balance analysis to assess the effects of genetic deletions on the fitness of the organism and its ability to produce essential biomolecules required for growth.
-
Citations
41 Claims
-
1-24. -24. (canceled)
-
25. A method performed in a computer of producing a genome specific stoichiometric matrix of a microbe, comprising:
-
obtaining a plurality of DNA sequences in a genome, wherein said plurality comprises a number of DNA sequences in a genome sufficient to produce an in silico representation of a microbe; determining open reading frames of genes in said plurality of DNA sequences; assigning a function to proteins encoded by said open reading frames by determining the homology of said open reading frames to gene sequences encoding proteins of known function; determining which of said open reading frames correspond to metabolic genes by determining if the assigned function of said proteins is involved in cellular metabolism; determining substrates, products and stoichiometry for each of said metabolic genes; and providing an output to a user of a genome specific stoichiometric matrix of said microbe produced from said substrates, products and stoichiometry. - View Dependent Claims (26, 27, 28, 29, 30, 31, 32)
-
-
33. A method performed in a computer for producing a genome specific stoichiometric matrix of a microbe, comprising:
-
a) providing a nucleotide sequence of a metabolic gene in the microbe; b) determining substrates, products and stoichiometry for said metabolic gene product based on its assigned function; c) repeating steps a) and b) for a plurality of metabolic genes of said microbe sufficient to produce an in silico representation; and d) providing an output to a user of a genome specific stoichiometric matrix produced from said substrates, products and stoichiometry of the metabolic genes product in said microbe. - View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41)
-
Specification