# Non-InterPro HMM databases

These archives contain profile-HMM databases used by the Atkinson laboratory
annotation pipeline but not distributed as part of the pipeline's InterPro
member-database collection.

## Databases

| Archive | Database | Models |
|---|---|---:|
| `ABCF_hmm_db.tar.gz` | ABCF | 45 |
| `AMR_hmm_db.tar.gz` | AMR | 743 |
| `AntiDefenseFinder_hmm_db.tar.gz` | AntiDefenseFinder | 178 |
| `DefenseFinder_hmm_db.tar.gz` | DefenseFinder | 1,000 |
| `NetFLAX_hmm_db.tar.gz` | NetFLAX | 310 |
| `PAT_hmm_db.tar.gz` | PAT | 384 |
| `PHROG_hmm_db.tar.gz` | PHROGs | 38,880 |
| `SAS_hmm_db.tar.gz` | SAS | 54 |
| `VFDB_hmm_db.tar.gz` | VFDB | 1,250 |

Pfam is not included here because Pfam 38.2 is distributed separately under
the InterPro member-database collection.

CDD is also distributed separately as a custom versioned database.

## Archive contents

Each archive contains:

- a combined HMMER profile database;
- `.h3f`, `.h3i`, `.h3m`, and `.h3p` files generated by `hmmpress`.

The pressed files allow HMMER and PyHMMER to load optimized profiles without
rebuilding the indexes after download.

## Metadata

Combined model-level metadata are provided separately at:

`../../metadata/non_interpro/non_interpro_hmm_metadata.tsv`

The metadata table uses the database and HMM model name as its join key.

## Provenance and licensing

These archives combine database content originating from several independent
projects. Each underlying database retains its original provenance, citation
requirements, and applicable license or terms.

The Atkinson laboratory prepared or packaged the HMMER database files for use
by the annotation pipeline. This does not imply ownership of the underlying
sequences, alignments, annotations, or biological database content.

Users are responsible for citing and complying with the terms of the relevant
source database.

## Integrity

`SHA256SUMS` contains checksums for the archives and this README.

No endorsement by the original database authors or distributors is implied.