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Nhoodie/hgt-real-mutation-pairs

HGT Real Mutation Pairs Real mutation pairs across 8 taxonomic domains for cross-domain horizontal gene transfer (HGT) mutation prediction. Dataset Details Split Pairs Mean mutation rate Mean distance train 3,317 ~4.2% ~6 nt test 826 ~1.2% 2.2 nt Domains Domain Sequences Rationale Archaea 1,260 Thermophile/halophile HGT Bacteria 630 Primary HGT domain Lichenes_HGT 210 Inter-kingdom HGT (fungi↔algae) Metazoa 1,680… See the full description on the dataset page: https://huggingface.co/datasets/Nhoodie/hgt-real-mutation-pairs.

sourceHugging Facemitupdated 6mo agoView on Hugging Face
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ℹ️ Dataset Note

This is the primary ground-truth dataset for HGT mutation prediction. It contains real biological mutation pairs with authentic HGT signatures (Ti/Tv ratio ~0.77, dominated by C>T and T>C transitions consistent with viral polymerase error patterns). This dataset is not affected by the ICI-DC degeneracy issues identified in synthetic datasets.

HGT Real Mutation Pairs

Real mutation pairs across 8 taxonomic domains for cross-domain horizontal gene transfer (HGT) mutation prediction.

Dataset Details

SplitPairsMean mutation rateMean distance
train3,317~4.2%~6 nt
test826~1.2%2.2 nt

Domains

DomainSequencesRationale
Archaea1,260Thermophile/halophile HGT
Bacteria630Primary HGT domain
Lichenes_HGT210Inter-kingdom HGT (fungi↔algae)
Metazoa1,680Microbiome HGT
Satellite_Viruses84Subviral agents
Viridiplantae420Limited bacterial→plant HGT
Viroids294Small RNA pathogens
Viruses420Phage transduction

Format

Each line is a JSON object:

json
{"parent": "ATGCGT...", "child": "ATGCGA...", "domain": "Bacteria", "distance": 3, "source_ids": ["AB123456"]}

Pipeline

  1. 1.Sequences fetched from NCBI with HGT-weighted sampling across 8 domains
  2. 2.Stop-codon-aware greedy chunking (~500bp)
  3. 3.Domain-aware nearest-neighbor pair building (C Levenshtein)
  4. 4.Leakage-free train/test split via connected-component clustering

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