# CDD HH-suite database: custom_2026_08

This is a custom HH-suite database constructed by the Atkinson laboratory
from multiple-sequence alignments distributed as part of the NCBI Conserved
Domain Database (CDD).

## Contents

- `cdd_custom_2026_08_a3m.ffdata`
- `cdd_custom_2026_08_a3m.ffindex`
- `cdd_custom_2026_08_hhm.ffdata`
- `cdd_custom_2026_08_hhm.ffindex`
- `cdd_custom_2026_08_cs219.ffdata`
- `cdd_custom_2026_08_cs219.ffindex`
- `cdd_metadata.tsv`
- `id_mapping.tsv`
- `SHA256SUMS`

The individual A3M alignments are contained in the A3M ffdata/ffindex pair
and are not distributed separately.

## Construction

CDD aligned FASTA files were converted to A3M format. The first
`lcl|consensus` sequence in each alignment defined the A3M match columns.
The first A3M header was rewritten to begin with the stable CDD accession,
followed by the CDD short name and description.

The database was constructed using HH-suite `hhsuitedb.py`.

## Model count

67,333 entries are present in each of the A3M, HHM, and CS219 indexes.

The model `pfam07590` was excluded because no corresponding record was
present in the supplied `cddid_all.tbl` metadata table.

Two length measurements are retained in `id_mapping.tsv`:

- the model length reported by CDD metadata;
- the number of match columns derived from the supplied CDD consensus.

These values can differ for some CDD records.

## Identifier and metadata coverage

Every HH-suite entry identifier corresponds to exactly one row in
`cdd_metadata.tsv`.

## Provenance

Source resource:

NCBI Conserved Domain Database (CDD)
https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

CDD includes NCBI-curated models and models imported from external resources,
including Pfam, SMART, COG, PRK, and TIGRFAMs. Ownership, attribution, citation,
and any applicable rights in the underlying source data remain with their
respective providers.

NCBI data usage policies:

https://www.ncbi.nlm.nih.gov/home/about/policies/

This directory contains a locally generated HH-suite conversion and is not an
official NCBI HH-suite distribution.

## Citation

Users should cite the appropriate NCBI CDD publication and the original
database publications relevant to the models used.

## Disclaimer

No endorsement by NCBI or any contributing database is implied.