| --- |
| 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) |
|
|
