# HH-suite databases

This directory contains HH-suite databases used by the Atkinson laboratory
annotation pipeline.

## Externally constructed and locally mirrored databases

### Pfam-A 38.2

Directory: `PfamA_v38_2/`

This database was not created by the Atkinson laboratory. It is mirrored for
reproducible use by the annotation pipeline.

Original distribution:

http://ftp.tuebingen.mpg.de/pub/ebio/protevo/toolkit/databases/hhsuite_dbs/PfamA_v38_2.tar.gz

Users may alternatively download it directly from the original distributor.
See `PfamA_v38_2/README.md` for provenance information.

### UniRef30 2023_02

Directory: `uniref/`

This database was not created by the Atkinson laboratory. It is mirrored for
reproducible use by the annotation pipeline.

Original distribution:

https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz

The original distribution states that these files are available under the
Creative Commons Attribution-ShareAlike 4.0 International License:

https://creativecommons.org/licenses/by-sa/4.0/

No modifications were made unless explicitly documented. See
`uniref/README.md` and `uniref/LICENSE.md`.

## Locally constructed HH-suite databases

The following HH-suite database files were constructed locally:

- `anti_defensefinder/`
- `cdd/`
- `defensefinder_hhsuitedb/`
- `netflax_hhsuitedb/`
- `pat_hhsuitedb/`
- `pdb/`
- `phrogs_hhsuitedb/`
- `sas_hhsuitedb/`

“Constructed locally” refers only to preparation of the HH-suite database
files. The underlying sequences, alignments, structures, annotations, and
database content retain their original provenance, attribution requirements,
and applicable terms.

Each database-specific directory should be consulted for source, construction,
citation, and licensing information.

## No endorsement

Mirroring or converting an external database does not imply endorsement by
its original authors, maintainers, or distributors.