README.md

---
pretty_name: SABmark
language:
- en
tags:
- protein
- sequence-alignment
- structural-biology
task_categories:
- other
configs:
- config_name: twi
  description: Twilight subset (<25% identity)
  data_files:
    - split: test
      path: twi.jsonl
- config_name: sup
  description: Superfamilies subset
  data_files:
    - split: test
      path: sup.jsonl
- config_name: twi_fp
  description: Twilight with added false positives
  data_files:
    - split: test
      path: twi_fp.jsonl
- config_name: sup_fp
  description: Superfamilies with added false positives
  data_files:
    - split: test
      path: sup_fp.jsonl
- config_name: all
  description: All subsets combined
  data_files:
    - split: test
      path: all.jsonl
---

# SABmark (Hugging Face Port)

Benchmark for protein sequence alignment under remote homology.

## Subsets

- `sup`: low-to-intermediate identity
- `twi`: very low identity (<25%)
- `sup_fp`: superfamilies with added false positives
- `twi_fp`: twilight with added false positives
- `all`: union of the above

## Features

- `pair_id`, `group_id`, `set_name`
- `seq1_id`, `seq2_id`, `seq1`, `seq2`
- `ref_alignment`: list of index pairs `[[i, j], ...]` (0-based)
- `percent_identity`, `scop_labels`, `meta`

## Usage

```python
from datasets import load_dataset
ds = load_dataset("DeepFoldProtein/SABmark", name="twi", split="test")  
ex = ds[0]
print(ex["seq1"], ex["seq2"], ex["ref_alignment"][:5])
```

## Citation

Please cite:

```bibtex
@article{VanWalle2004SABmark,
  title={SABmark---a benchmark for sequence alignment that covers the entire known fold space},
  author={Van Walle, Ivan and Lasters, Ignace and Wyns, Lode},
  journal={Bioinformatics},
  volume={21},
  number={7},
  pages={1267--1268},
  year={2004},
  publisher={Oxford University Press},
  DOI = {10.1093/bioinformatics/bth493}
}
```

---

### `dataset_infos.json` — stub (optional but nice)

```json
{
  "twi": {
    "description": "SABmark Twilight subset (<25% identity).",
    "features": {
      "pair_id": {"dtype": "string", "_type": "Value"},
      "group_id": {"dtype": "string", "_type": "Value"},
      "set_name": {"names": ["twi", "sup", "twi_fp", "sup_fp"], "_type": "ClassLabel"},
      "seq1_id": {"dtype": "string", "_type": "Value"},
      "seq2_id": {"dtype": "string", "_type": "Value"},
      "seq1": {"dtype": "string", "_type": "Value"},
      "seq2": {"dtype": "string", "_type": "Value"},
      "ref_alignment": {"feature": {"feature": {"dtype": "int32", "_type": "Value"}, "_type": "Sequence"}, "_type": "Sequence"},
      "percent_identity": {"dtype": "float32", "_type": "Value"},
      "scop_labels": {"feature": {"dtype": "string", "_type": "Value"}, "_type": "Sequence"},
      "meta": {"dtype": "string", "_type": "Value"}
    }
  }
}
```