anvi-setup-modelseed-database

This program downloads and sets up the ModelSEED Biochemistry database..

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Authors

Can consume

functions

Can provide

reaction-ref-data

Usage

This program downloads and sets up the latest version of the ModelSEED Biochemistry database.

The ModelSEED Biochemistry database consists of two tab-delimited files of reaction and compound data, respectively, and is valuable due to harmonization of IDs and properties from multiple reference databases commonly used in metabolic modeling.

anvi-reaction-network relies upon ModelSEED Biochemistry in conjunction with the KEGG Orthology database. KEGG Orthology (KO) protein annotations of genes are associated with predicted enzymatic reactions. These KEGG reactions are cross-referenced to the ModelSEED Biochemistry database to retrieve information on properties including reaction stoichiometry and reversibility. anvi-reaction-network stores reactions and metabolites thereby predicted in the contigs-db for the genome. The program, anvi-setup-kegg-data, sets up the requisite KO database.

Usage

The simplest anvi-setup-modelseed-database command sets up the database in the default anvi’o ModelSEED data directory.

A custom directory can be provided instead. Within the provided directory, a subdirectory named ModelSEED is created for storage of the database.

Finally, in conjunction with either of the previous commands, the --reset flag can be used to delete any existing target database directory and its contents before setting up the latest version of the ModelSEED Biochemistry database there.

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Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.