macwiatrak/bacbench-strain-clustering-protein-sequences

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. 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.

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 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 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: genomesampleaccession dtype: string
• —name: genomestudyaccession dtype: string
• —name: country dtype: string
• —name: family dtype: string
• —name: genus dtype: string
• —name: species dtype: string splits:
• —name: test numbytes: 53088486516 numexamples: 60710 downloadsize: 49650872351 datasetsize: 53088486516 configs:
• —configname: default datafiles:
• —split: test path: data/test-* ---