Dataset Viewer
pair_id
stringlengths 22
24
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values | set_name
stringclasses 4
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group100:d1d5ra2-d1vhra_
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group100:d1eeoa_-d1fpza_
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group100
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group100:d1eeoa_
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group100:d1fpza_
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TPIHISWLSLSRVNCSQFLGLCALPGCKFKDVRRNVQKDTEELKSCGIQDIFVFCTRGELSKYRVPNLLDLYQQCGIITHHHPIADGGTPDIASCCEIMEELTTCLKNYRKTLIHSYGGLGRSCLVAACLLLYLSDTISPEQAIDSLRDLRGSGAIQTIKQYNYLHEFRDKLAAHL
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group100:d1eeoa_-d1lyva_
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group100
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twi
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group100:d1eeoa_
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group100:d1lyva_
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group100:d1eeoa_-d1ohea1
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group100
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twi
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group100:d1eeoa_
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group100:d1ohea1
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group100:d1fpza_-d1ohea1
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group100:d1fpza_-d1vhra_
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group100
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twi
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group100:d1vhra_
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group100:d1lyva_-d1ohea1
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group100
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twi
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group100:d1ohea1
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group101:d1a8l_1-d1a8y_2
|
group101
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twi
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group101:d1a8l_1
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group101:d1a8y_2
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MGLISDADKKVIKEEFFSKMVNPVKLIVFVRKDHCQYCDQLKQLVQELSELTDKLSYEIVDFDTPEGKELAKRYRIDRAPATTITQDGKDFGVRYFGLPAGHEFAAFLEDIVDVSREET
|
VELIEGERELQAFENIEDEIKLIGYFKNKDSEHYKAFKEAAEEFHPYIPFFATFDSKVAKKLTLKLNEIDFYEAFMEEPVTIPDKPNSEEEIVNFVEEHRRS
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|
group101:d1a8l_1-d1aba__
|
group101
|
twi
|
group101:d1a8l_1
|
group101:d1aba__
|
MGLISDADKKVIKEEFFSKMVNPVKLIVFVRKDHCQYCDQLKQLVQELSELTDKLSYEIVDFDTPEGKELAKRYRIDRAPATTITQDGKDFGVRYFGLPAGHEFAAFLEDIVDVSREET
|
MFKVYGYDSNIHKCGPCDNAKRLLTVKKQPFEFINIMPEKGVFDDEKIAELLTKLGRDTQIGLTMPQVFAPDGSHIGGFDQLREYFK
|
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] | 10.9375 |
[
"class:51349",
"fold:52832",
"superfamily:52833",
"family:52849",
"domain:52850",
"species:52852",
"protein:32777"
] |
{"length1": 119, "length2": 87, "true_pos1": 1, "true_pos2": 1, "source_file": "d1a8l_1-d1aba__.fasta"}
|
End of preview. Expand
in Data Studio
SABmark (Hugging Face Port)
Benchmark for protein sequence alignment under remote homology.
Subsets
sup: low-to-intermediate identitytwi: very low identity (<25%)sup_fp: superfamilies with added false positivestwi_fp: twilight with added false positivesall: union of the above
Features
pair_id,group_id,set_nameseq1_id,seq2_id,seq1,seq2ref_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"}
}
}
}
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