cssbsnu/Thal-Kak_local_db

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

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`, under Changes.

mmseqs/ — MMseqs2 expandable profile databases

Searched by --msa mmseqs_local. The .idx search index is not shipped — install_db.sh builds it locally, which is where the third size column goes.

hhblits/ — HH-suite (FFindex) databases

Searched by --msa hhblits_local.

template/ — local template-search snapshot

Used when template.enable: true in the MSA config (the default on both local engines).

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.

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.shfrom Thal-Kak

The installer resolves the archive, downloads it, 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.

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.

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.

Everything, all four families: 5.42 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`. The summary:

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` carries its Cite line, and for the CC BY / CC BY-SA archives that attribution is a licence condition. For the pipeline that searches them, cite: Bae J. et al. Thal-Kak: unifying biomolecular structure predictors reveals a sampling–selection gap. bioRxiv 2026.08.19.745680 (2026). doi:10.64898/2026.08.19.745680

@article{bae2026thal, title={Thal-Kak: unifying biomolecular structure predictors reveals a sampling-selection gap}, author={Bae, Junhyeok and Jo, Soohyun and Kim, Yeajin and Kim, Dongyun and Kim, Kwanwook and Park, Sanghyun and Park, Sanggeun and Myung, Sojung and Shin, Hyunho and Kim, Min Hyeok and others}, journal={bioRxiv}, pages={2026--08}, year={2026}, publisher={Cold Spring Harbor Laboratory} }

Links

• —Pipeline: <https://github.com/CSSB-SNU/Thal-Kak>
• —Installer documentation: install/README.md in that repository
• —Per-archive provenance and licensing: `LICENSE.txt`