FOAM: Functional Ontology Assignments for Metagenomes, a Hidden Markov Model (HMM) database with environmental focus
In this repersitory you'll find script to run the HMM database that we developed with @bioman (E. Prestat) in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231724/
The database itself (7G) and can be downloaded here: http://cbb.pnnl.gov/portal/software/FOAM.html
Now on OSF (August 2019): https://osf.io/5ba2v/
Along with the Ontology (important) and the alignments (if you want to go dig into that).
WARNING: the format of the HMM only work with HMMER 3.0. If you want to use it with another verison, email me, there are a few changes to do.
You will just have to download the database, and you can use one of the scripts here to run your annotation. Have fun! Let me know if you have any question: raw937@gmail.com