functions [artifact]

A CONCEPT-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-import-functions anvi-run-kegg-kofams anvi-run-ncbi-cogs anvi-run-pfams

Required or used by

anvi-analyze-synteny anvi-export-functions

Description

This artifact contains information about the functions of the genes in your contigs-db.

It is a table within your contigs-db that contains functional annotations for your genes.

To get one of these for your contigs-db, you can either import it (using anvi-import-functions) or make one yourself by running your contigs against one of two databases available in anvi’o:

• NCBI COGs database – see anvi-run-ncbi-cogs for instructions
• EBI’s Pfam database – see anvi-run-pfams for instructions
• The KOfamKOALA database – see anvi-run-kegg-kofams for instructions. Functions specifically from the KOfam database are used to run anvi-estimate-metabolism and are also called kegg-functions.

You can also use EggNOG or InterProScan and then import the results into anvi’o, as described in this blog post.

This is used to run anvi-analyze-synteny.

You can also use anvi-export-functions to obtain a file containing these functional annotations through a functions-txt artifact.

Edit this file to update this information.