Run Pfam on Contigs Database.
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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.
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