functions

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-cazymes anvi-run-kegg-kofams anvi-run-ncbi-cogs anvi-run-pfams

Required or used by

anvi-analyze-synteny anvi-compute-functional-enrichment-across-genomes anvi-compute-functional-enrichment-in-pan anvi-compute-metabolic-enrichment anvi-delete-functions anvi-display-functions anvi-export-functions anvi-setup-modelseed-database anvi-script-gen-function-matrix-across-genomes anvi-script-gen-functions-per-group-stats-output

Description

This is an artifact that describes annotation of genes in your contigs-db with functions.

Broadly used across anvi’o, functions are one of the most essential pieces of information stored in any contigs-db. To see what annotation sources for functions are available in a given contigs-db or genomes-storage-db, you can use the program anvi-db-info.

To populate a given contigs-db with functions, anvi’o includes multiple programs that can annotate genes using various sources of annotation. These programs include,

• anvi-run-ncbi-cogs, which uses NCBI’s COGs database,
• anvi-run-pfams, which uses EBI’s Pfam database,
• anvi-run-cazymes, which uses the dbCAN CAZyme HMMs
• anvi-run-kegg-kofams, which uses the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and produces kegg-functions, which is the necessary annotation information that can be used by the program anvi-estimate-metabolism.

In addition, you can use the program anvi-import-functions with a simple functions-txt to import functions from any other annotation source, or to import any ad hoc, user-defined function to later access through anvi’o interfaces or programs.

You can use anvi-import-functions also to import functions from EggNOG or InterProScan as described in this blog post.

You can also use anvi-export-functions to obtain a file containing these functional annotations through a functions-txt artifact, and use anvi-display-functions to show the distribution of functions across multiple contigs-dbs.

Edit this file to update this information.