README.md

metadata

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

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:

@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)

{
  "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"}
    }
  }
}