Run dbCAN CAZymes on contigs-db.
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Before you run this program, you’ll have to set up the CAZyme database on your computer with the program anvi-setup-cazymes.
The CAZyme 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
anvi-run-cazymes -c contigs-db
By default, this uses
hmmsearch to run HMMs. You can choose to use
hmmscan instead by running
Use the parameter
--noise-cutoff-terms to filter out hits. The default value is
--noise-cutoff-terms -E 1e-12. If you want to explore filtering options, check out the help menu of the underlying hmm program you are using e.g.
anvi-run-cazymes -c contigs-db \ --noise-cutoff-terms “-E 1e-14”
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.