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A metabolic reconstruction provides a highly mathematical, structured platform on which to understand the systems biology of metabolic pathways within an organism. [2] The integration of biochemical metabolic pathways with rapidly available, annotated genome sequences has developed what are called genome-scale metabolic models.
Genome-scale reconstructions describe all the biochemical reactions in an organism based on its entire genome. These reconstructions model metabolism by focusing on the interactions between metabolites , identifying which metabolites are involved in the various reactions taking place in a cell or organism, and determining the genes that encode ...
Here, two studies are highlighted which show two different varieties of uses, one on a genome scale and other on identifying specific SNPs (Single Nucleotide Polymorphisms) within a genome. AlgaGEM. AlgaGEM is a genome scale metabolic network model for a compartmentalized algae cell developed by Gomes de Oliveira Dal’Molin et al. [7] based on ...
MetaNetX is a database maintained by the SIB Swiss Institute of Bioinformatics for the automated model construction, and the genome annotation for large-scale metabolic networks. MetaNetX provides a number of tools to access, analyse and manipulate metabolic networks. [1] MetaNetX provides a bunch of pre-mapped metabolic models.
Within the stoichiometric paradigm, a number of relatively simple linear algebra methods use restricted metabolic networks or genome-scale metabolic network models to perform flux balance analysis and the array of techniques derived from it. These linear equations are useful for steady state conditions.
In practice, researchers may select an existing library depending on their experimental purpose and cell lines of interest. As of February 2020, the most widely used resources for genome-wide CRISPR knockout screens have been the two Genome-Scale CRISPR Knock-Out (GeCKO) libraries created by the Zhang lab. [35]
Ensembl Genomes: provides genome-scale data for bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces (using the Ensembl software platform) FlyBase: genome of the model organism Drosophila melanogaster; Gene Disease Database
Software to build and analyze ensembles of genome-scale metabolic network reconstructions [61] Systems biology: Gregory L. Medlock, Thomas J. Moutinho, Jason A. Papin: 2001 Molecular Evolutionary Genetics Analysis (MEGA) Provides multiple algorithms to construct phylogenetic trees, including UPGMA, Maximum Likelihood, Maximum Parsimony, etc