cssbsnu/Thal-Kak_local_db

Thal-Kak local MSA, template databases

The sequence and template databases that the local MSA modes of 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, 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 0.99 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.

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.

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	489.8 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.

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).

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.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.

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	1.48 TiB installed here (1.84 TiB with uniref30_2302)
template	1 of 1	81.2 GiB
rna	0 of 2	28.1 GiB, built locally

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:

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 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