Matthew Schechter

Ok I made some minor adjustments but did not push the commit. Let me know if/when it's ok to push :)

Hi @iwilkie, thanks for the question! [anvi-run-cazymes](https://anvio.org/help/main/programs/anvi-run-cazymes/) only runs the HMMs from dbCAN2 across the amino acids sequences in a [contigs-db](https://anvio.org/help/7/artifacts/contigs-db/) with hmmscan or hmmsearch. However, you can use [anvi-import-functions](https://anvio.org/help/7/programs/anvi-import-functions/)...

@iwilkie I started working on this feature request [here](https://github.com/merenlab/anvio/tree/upgrade-to-dbCAN3) and got confused about where I can find dbCAN3 files, in particular, the dbCAN-sub HMMs. Is this the dbCAN3 [dbCAN_sub](https://bcb.unl.edu/dbCAN2/download/Databases/dbCAN_sub.hmm) file?...

Thanks for the input @xvazquezc! > Coming back to the files, the one you indicate is the dbCAN-sub HMM, [this one is the current dbCAN HMM](https://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V12.txt) (barely one month old)....

@xvazquezc thank you very much for breaking this down for the anvi'o community! > About the files, this is the current dbCAN HMM: https://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V12.txt, and this is the dbCAN-sub HMM:...

> If I am understanding correctly, dbCAN-sub is another set of HMMs that provides more specific gene annotations? > If so, then it doesn't directly have a place in metabolism...

@meren to finish this feature request, I need to incorporate two HMM files into `anvi-run-cazymes`: - [dbCAN-HMMdb-V12.txt](https://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V12.txt) - [dbCAN_sub.hmm](https://bcb.unl.edu/dbCAN2/download/Databases/dbCAN_sub.hmm) I am currently working on this branch [upgrade-to-dbCAN3](https://github.com/merenlab/anvio/tree/upgrade-to-dbCAN3). [dbCAN-HMMdb-V12.txt](https://bcb.unl.edu/dbCAN2/download/dbCAN-HMMdb-V12.txt) is already...

Thanks for pointing this out @xvazquezc! That definitely answers my question :)

We can address #2148 in this branch :)

Thanks for incorporating `anvi-run-cazymes` into your anvi'o metabolism framework and finding ways to optimize the program! > In my opinion, the expected behavior here would be to use the ID...