---
license: apache-2.0
tags:
- bacteria
- biology
- proteins
- prokaryotes
- genomics
- genomes
pretty_name: Dataset for clustering whole bacterial genomes (protein sequences)
size_categories:
- 10K<n<100K
---
# Dataset for whole-bacterial genomes clustering (Protein sequences)

A dataset of 60,710 bacterial genomes across 25 species, 10 genera and 7 families.

The genome protein sequences have been extracted from [MGnify](https://www.ebi.ac.uk/metagenomics). Each row contains a set of contigs with protein sequences present in the genome.
Each contig is a list of proteins ordered by their location on the chromosome or plasmid.


## Labels
The species, genus and family labels have been provided by MGnify

## Usage
We recommend loading the dataset in a streaming mode to prevent memory errors.
```python
import itertools

from datasets import load_dataset


ds = load_dataset("macwiatrak/bacbench-strain-clustering-protein-sequences", split="test", streaming=True)

# fetch the protein sequence of the genome
item = next(iter(ds))
# all proteins present in the genome across contigs
prot_seqs_contigs = item["protein_sequence"]
# get protein sequences for a single contig
prot_seqs = prot_seqs_contigs[0]
# flatten all proteins present in the genome across all contigs
prot_seqs_flat = list(itertools.chain(*prot_seqs_contigs))
```

## Split

The strain clustering task is a fully unsupervised task, therefore, we do not perform any split and the whole dataset is available as part of the `test` split.

See [github repository](https://github.com/macwiatrak/Bacbench) for details on how to embed the dataset with DNA and protein language models as well as code to predict antibiotic
resistance from sequence. For DNA sequence representation of the genome see the [strain-clustering-dna](https://huggingface.co/datasets/macwiatrak/bacbench-strain-clustering-dna)
dataset.

---
dataset_info:
  features:
  - name: genome_name
    dtype: string
  - name: contig_name
    sequence: string
  - name: start
    sequence:
      sequence: string
  - name: end
    sequence:
      sequence: string
  - name: locus_tag
    sequence:
      sequence: string
  - name: protein_sequence
    sequence:
      sequence: string
  - name: strand
    sequence:
      sequence: string
  - name: genome_completeness
    dtype: string
  - name: genome_lineage
    dtype: string
  - name: genome_sample_accession
    dtype: string
  - name: genome_study_accession
    dtype: string
  - name: country
    dtype: string
  - name: family
    dtype: string
  - name: genus
    dtype: string
  - name: species
    dtype: string
  splits:
  - name: test
    num_bytes: 53088486516
    num_examples: 60710
  download_size: 49650872351
  dataset_size: 53088486516
configs:
- config_name: default
  data_files:
  - split: test
    path: data/test-*
---