reaction-ref-data

A DB-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-setup-modelseed-database

Required by

There are no anvi’o tools that require this artifact directly, which means it is most likely an end-product for the user.

Can be used by

anvi-predict-metabolic-exchanges anvi-reaction-network

Description

Reference databases required for anvi-reaction-network are stored in directories of downloaded files set up by anvi-setup-modelseed-database and anvi-setup-kegg-data.

anvi-reaction-network currently relies upon comparison of KEGG Orthology (KO) gene annotations (kegg-functions) stored in a contigs-db to reference databases: KEGG KO and ModelSEED Biochemistry. The ModelSEED Biochemistry database harmonizes and consolidates reference data from multiple sources, including KEGG, in two comprehensive tables of reactions and compounds.

The KEGG databases (kegg-data) can be obtained by running anvi-setup-kegg-data, and the ModelSEED database can be obtained by running anvi-setup-modelseed-database.

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