README.md

---
viewer: false
license: other
license_name: mixed-per-archive
license_link: https://huggingface.co/datasets/cssbsnu/Thal-Kak_local_db/blob/main/LICENSE.txt
language:
- en
pretty_name: Thal-kak local MSA, template DB
size_categories:
- 100B<n<1T
tags:
- MSA
- template
- protein
- NA
---

# Thal-Kak local MSA, template databases

The sequence and template databases that the local MSA modes of
**[Thal-Kak](https://github.com/CSSB-SNU/Thal-Kak)** search —
`--msa mmseqs_local`, `--msa hhblits_local`, `--msa mmseqs_hhblits_local`, and
local template search on any of them.

> **Install these with [`install_db.sh`](#getting-the-databases), not by hand.**
> Every file here is a multi-gigabyte `.tar.zst` holding a prebuilt MMseqs2 or
> HH-suite database; the installer verifies it, unpacks it into place and
> renames the files to the layout the pipeline expects.

## At a glance

| | |
|---|---|
| Archives | 12 (`mmseqs/` 5, `hhblits/` 6, `template/` 1) |
| Download | **664 GiB** total |
| After extraction | 2.31 TiB, plus 0.97 TiB of MMseqs2 search indexes built on your machine |
| Compression | zstd (`zstd` required to unpack) |
| Licenses | mixed, per archive — CC0 1.0 / CC BY 4.0 / CC BY-SA 4.0 / **no grant** (Logan). See [License and attribution](#license-and-attribution). |

## What is in this repository

> **These are derived databases, not upstream mirrors.** Each archive was
> re-clustered and/or reformatted here, so the counts below are ours and will
> not match numbers computed on the upstream distribution. What was changed is
> recorded per source in [`LICENSE.txt`](https://huggingface.co/datasets/cssbsnu/Thal-Kak_local_db/blob/main/LICENSE.txt), under `Changes`.

### `mmseqs/` — MMseqs2 [expandable profile databases](https://github.com/soedinglab/MMseqs2/wiki#expandable-profile-databases)

Searched by `--msa mmseqs_local`. Two layers: *representatives* are what the
prefilter scans, *members* are what `expandaln` can pull into the alignment.
The `.idx` search index is **not** shipped — `install_db.sh` builds it locally,
which is where the third size column goes.

| Archive | Download | Extracted | Index (local) | Representatives | Members |
|---|--:|--:|--:|--:|--:|
| `uniref100_2026_01.tar.zst` | 130.3 GiB | 211.4 GiB | 277.8 GiB | 39,312,380 | 475,217,233 |
| `mgnify_clusters.tar.zst` | 126.9 GiB | 202.3 GiB | 470.8 GiB | 313,067,917 | 717,738,164 |
| `envhog_std.tar.zst` | 20.7 GiB | 36.7 GiB | 53.6 GiB | 11,742,979 | 129,896,064 |
| `bfd_reduced.tar.zst` | 18.6 GiB | 27.6 GiB | 114.7 GiB | 51,652,611 | 65,984,053 |
| `logan_human.tar.zst` | 12.0 GiB | 28.1 GiB | 73.9 GiB | 61,657,544 | 71,364,503 |

### `hhblits/` — HH-suite (FFindex) databases

Searched by `--msa hhblits_local`. All but `envhog` were converted here from the
corresponding MMseqs2 database, with cs219 and hhm profiles computed here;
`envhog` is upstream's own HH-suite build.

| Archive | Download | Extracted | Clusters (cs219) | Member sequences |
|---|--:|--:|--:|--:|
| `uniref100.tar.zst` | 157.2 GiB | 1,301.5 GiB | 39,312,371 | 475,217,228 |
| `uniref30_2023_02.tar.zst` | 54.8 GiB | 261.2 GiB | 36,293,491 | 330,676,110 |
| `mgnify_clusters.tar.zst` | 33.7 GiB | 150.3 GiB | 31,779,642 | 278,185,288 |
| `logan_nonhuman.tar.zst` | 24.2 GiB | 55.9 GiB | 28,702,814 | 130,348,747 |
| `envhog.tar.zst` | 4.7 GiB | 11.5 GiB | 2,203,457 | 25,550,069 |
| `logan_human.tar.zst` | 0.8 GiB | 2.0 GiB | 1,645,263 | 7,385,713 |

### `template/` — local template-search snapshot

Used when `template.enable: true` in the MSA config (the default on both local
engines). A wwPDB/RCSB snapshot repackaged as a protein-only seqres FASTA, an
MMseqs2 search database, per-entry gzipped mmCIF, a chain-metadata table and a
deposition-date table.

| Archive | Download | Extracted | Cutoff | PDB entries | Protein chains | Unique sequences |
|---|--:|--:|---|--:|--:|--:|
| `BioMolDB_20260224.tar.zst` | 80.5 GiB | 81.2 GiB | 2026-02-24 | 244,541 | 1,025,280 | 178,610 |

## What is *not* here

`install_db.sh` can install four more databases, and fetches those from the
upstream provider directly — nothing of them is redistributed here.

| Installer command | Fetched from |
|---|---|
| `--family mmseqs uniref30_2302` | `opendata.mmseqs.org` (the ColabFold build) |
| `--family hhblits bfd` | `storage.googleapis.com/alphafold-databases` (full BFD) |
| `--family rna rfam` | EMBL-EBI |
| `--family rna rnacentral` | EMBL-EBI |

Three consequences worth knowing before you plan a download:

- **Heteromers on `hhblits_local` also need the MMseqs2 `uniref30_2302`.** The
  HH-suite UniRef100 carries no taxonomy, so multimer pairing is delegated to
  mmseqs, which needs that database's `db_mapping` / `db_taxonomy` sidecars.
- **`logan_nonhuman` exists in HH-suite format only.** Its MMseqs2 build
  extracts to 1.4 TB and is not published anywhere. This asymmetry is
  deliberate.
- **RNA and RNP targets need the `rna` family**, which is not here at all — it
  is built locally from Rfam and RNAcentral.

## Getting the databases

### With `install_db.sh` (recommended)

The installer resolves the archive, downloads it, verifies its SHA-256 against
`install/manifest/databases.tsv`, extracts it into place atomically, normalizes
the file stems to the layout `db_paths.yaml` expects, and builds the MMseqs2
`.idx` where one is needed. It is idempotent and resumable.

```bash
git clone https://github.com/CSSB-SNU/Thal-Kak.git
cd Thal-Kak
# create and activate the project environment first — it provides
# zstd, aria2c and mmseqs, which the installer calls.

./install_db.sh --family mmseqs                            # every mmseqs archive
./install_db.sh --family mmseqs uniref100_2026_01          # just this one
./install_db.sh --family hhblits envhog logan_human        # several by name
./install_db.sh --family template
./install_db.sh --family all                               # all four families
./install_db.sh --family mmseqs --status                   # what is already installed
```

To install somewhere other than `<repo>/db`, edit `db_paths.yaml` **before**
running the installer — it reads that file and never writes it.

### Manually

```bash
pip install -U "huggingface_hub[cli]"

hf download cssbsnu/Thal-Kak_local_db --repo-type dataset \
    --include "hhblits/envhog.tar.zst" "LICENSE.txt" --local-dir ./dl
```

`--include` filters the whole repo, so name `LICENSE.txt` alongside the archives —
otherwise the terms that govern what you just downloaded stay behind on the
Hub. A plain `hf download <repo> --repo-type dataset` takes everything and
needs no such care.

Unpacking by hand is possible (`zstd -dc <archive> | tar -x -C <dir>`) but you
then have to reproduce the layout yourself: each database lives at
`<family root>/<key>/`, with every file inside renamed from its build-time stem
to `db` (`UniRef30_2023_02_a3m.ffdata` → `db_a3m.ffdata`, and so on).
`install_db.sh` does that rename for you. Prefer it unless you are mirroring.

## Disk budget

Peak usage is higher than the final figure, because an archive sits on disk next
to the tree being unpacked from it. Installing one family at a time keeps that
overhead to a single archive.

| Family | Archives here | Installed size |
|---|--:|--:|
| `hhblits` | 6 of 7 | 1.74 TiB installed here (3.47 TiB with the full BFD) |
| `mmseqs` | 5 of 6 | 1.46 TiB installed here (1.82 TiB with `uniref30_2302`) |
| `template` | 1 of 1 | 81.2 GiB |
| `rna` | 0 of 2 | 27.9 GiB, built locally |

Everything, all four families: **5.40 TiB** installed, ~5.7 TiB peak when
installed family by family.

## License and attribution

**The Apache-2.0 license on the Thal-Kak source code does not apply to anything
in this repository.** Each archive carries the license of the source it derives
from; no archive mixes sources. The authoritative record — upstream license,
the license we place on our archive, attribution, citation, and exactly what we
changed — is [`LICENSE.txt`](https://huggingface.co/datasets/cssbsnu/Thal-Kak_local_db/blob/main/LICENSE.txt). The summary:

| Archives | License we grant | Source |
|---|---|---|
| `mmseqs/uniref100_2026_01`, `hhblits/uniref100` | CC BY 4.0 | UniProt UniRef100, release 2026_01 |
| `hhblits/uniref30_2023_02` | CC BY-SA 4.0 | UniRef30 2023_02, as built by ColabFold |
| `mmseqs/bfd_reduced` | CC BY-SA 4.0 | BFD reduced subset, via the AlphaFold databases |
| `mmseqs/mgnify_clusters`, `hhblits/mgnify_clusters` | CC0 1.0 | MGnify protein database, release 2024_04 |
| `mmseqs/envhog_std`, `hhblits/envhog` | CC BY 4.0 | EnVhogDB |
| `mmseqs/logan_human`, `hhblits/logan_human`, `hhblits/logan_nonhuman` | **none** | Logan v1 (SRA cutoff 2023-12-10) |
| `template/BioMolDB_20260224` | CC0 1.0 | wwPDB / RCSB PDB, snapshot 2026-02-24 |

Three things that are easy to miss:

- **The Logan archives carry no license grant.** No license instrument has been
  applied to that data by its distributor, so we grant no rights in it and make
  no representation about your right to use or redistribute it. It is passed
  through subject to the NCBI notice reproduced in `LICENSE.txt`, entry 6.
- **We do not license the output of the pipeline.** An alignment or template
  file produced by a run contains material from whichever databases you
  searched. We make no claim over it either.
- **Two license claims are disputed upstream** (`uniref30_2302`, `bfd_reduced`).
  Both disputes are written out in `LICENSE.txt`; we follow the more restrictive
  claim for anything we redistribute.

Everything here is provided **AS IS, WITHOUT WARRANTY OF ANY KIND**, either by
the upstream provider or by us, and without any representation that it is fit
for a particular purpose.

## Citing

Cite the upstream database for whichever archive you used — each entry in
[`LICENSE.txt`](https://huggingface.co/datasets/cssbsnu/Thal-Kak_local_db/blob/main/LICENSE.txt) carries its `Cite` line. For the pipeline itself, see the
[Thal-Kak repository](https://github.com/CSSB-SNU/Thal-Kak).

## Links

- Pipeline: <https://github.com/CSSB-SNU/Thal-Kak>
- Installer documentation: `install/README.md` in that repository
- Per-archive provenance and licensing: [`LICENSE.txt`](https://huggingface.co/datasets/cssbsnu/Thal-Kak_local_db/blob/main/LICENSE.txt)