Release 12.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available for download. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
What’s new?
The 12.0 release contains:
- 15,849 HMMs maintained by NCBI
- 271 new HMMs since release 11.0
- 1,248 HMMs with better names, EC numbers, Gene Ontology (GO) terms, gene symbols or publications
You can search and view the details for these in the Protein Family Model collection, which also includes conserved domain architectures and BlastRules, and find all RefSeq proteins these name.
GO terms associated with HMMs are now propagated to CDSs and proteins annotated with PGAP. In case you missed it, see our previous blog post on this topic.
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We want to hear from you!
If you have questions or would like to provide feedback, please reach out to us at info@ncbi.nlm.nih.gov.
I was playing around with this release and downloaded all the models. I tried to concatenate them in a single hmm library but I had a problem with hmmpress because there are two versions of one of the models (name: PRK02220.1): NF002571.0 and NF002571.1. I think the older version should be removed?
Thanks for your comment. We encourage you to contact our help desk so we can address this issue: info@ncbi.nlm.nih.gov