AllTheBacteria/BacCorpus-intergenic-dna-90

BacCorpus Intergenic DNA 90

BacCorpus Intergenic DNA 90 is a large-scale, sequence-level clustered dataset of bacterial intergenic DNA regions. It contains representative intergenic DNA sequences clustered at 90% sequence identity and 90% coverage, derived from BacCorpus, a uniformly processed bacterial genome resource spanning millions of quality-controlled isolate genomes and metagenome-assembled genomes.

This dataset is intended for training and evaluating DNA or mixed-modality genomic language models on bacterial non-coding sequence. In bacterial genomes, intergenic regions can contain regulatory and organisational signals such as promoters, terminators, and spacing between neighbouring genes, making them useful for genome-aware representation learning.

BacCorpus Intergenic DNA 90 was built by combining genomes from several public bacterial genome resources, including MGnify [1], SPIRE [2], HRGM [3], GTDB [4], mOTUs DB [5], and AllTheBacteria [6], annotating the genomes, extracting the intergenic regions and clustering them with MMSeqs2 (version 18.8cc5c).

Intended Uses

This dataset is intended for:

• pretraining DNA language models on bacterial intergenic sequence;
• training mixed protein-DNA genomic language models;
• studying bacterial regulatory and non-coding sequence variation;
• sampling representative bacterial intergenic DNA for downstream model training;
• evaluating sequence redundancy reduction strategies for bacterial genomics.

How to Use

Because this dataset is large, we recommend streaming it rather than downloading it locally.

from datasets import load_dataset

ds = load_dataset(
    "AllTheBacteria/BacCorpus-intergenic-dna-90",
    split="train",
    streaming=True,
)

example = next(iter(ds))
print(example.keys())
print(example)

Citation:

TBD

References

[1] Richardson, L. et al. MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Research 51(D1), D753–D759 (2023). doi:10.1093/nar/gkac1080

[2] Schmidt, T. S. B. et al. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Research 52(D1), D777–D783 (2024). doi:10.1093/nar/gkad943

[3] Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology 39, 105–114 (2021). doi:10.1038/s41587-020-0603-3

[4] Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research 50(D1), D785–D794 (2022). doi:10.1093/nar/gkab776

[5] Dmitrijeva, M. et al. The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities. Nucleic Acids Research 53(D1), D797–D805 (2025). doi:10.1093/nar/gkae1004

[6] Hunt, M. et al. AllTheBacteria – all bacterial genomes assembled, available, and searchable. bioRxiv (2024). doi:10.1101/2024.03.08.584059