Microbial 'omics

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# anvi-run-pfams [program]

Run Pfam on Contigs Database.

See program help menu or go back to the main page of anvi’o programs and artifacts.

## Usage

This program associates genes in your contigs-db with functions using the EBI’s Pfam database.

Before you run this program, you’ll have to set up the Pfam database on your computer with the program anvi-setup-pfams.

The Pfam database is based on protein sequences, so anvi’o will convert your genetic information into protein sequences and then use HMMs to compare them to the database.

Unsure what an HMM is? Check out our vocab page

To run, you’ll need to provide a contigs-db. If you stored the pfams-data that you got from running anvi-setup-pfams in a custom location, you’ll need to provide that path as well. The output is a functions artifact.

Here is a default run:

anvi-run-ncbi-cogs -c contigs-db \ --pfam-data-dir pfams-data

By default, this uses hmmsearch to run HMMs. You can choose to use hmmscan instead by running

anvi-run-ncbi-cogs -c contigs-db \ --pfam-data-dir pfams-data \ --hmmer-program hmmscan

See this article for a discussion on the performance of the two HMMER programs.

Edit this file to update this information.

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.