dataset_info:
features:
- name: genome_name
dtype: string
- name: contig_name
sequence: string
- name: protein_id
sequence:
sequence: string
- name: protein_sequence
sequence:
sequence: string
- name: taxid
dtype: string
- name: locus_tag
sequence:
sequence: string
- name: start
sequence:
sequence: int64
- name: end
sequence:
sequence: int64
- name: product
sequence:
sequence: string
- name: label
dtype: float64
splits:
- name: train
num_bytes: 778412387
num_examples: 618
- name: validation
num_bytes: 261143933
num_examples: 206
- name: test
num_bytes: 242498068
num_examples: 206
download_size: 1090641715
dataset_size: 1282054388
configs:
- config_name: default
data_files:
- split: train
path: data/train-*
- split: validation
path: data/validation-*
- split: test
path: data/test-*
license: apache-2.0
pretty_name: >-
Dataset for predicting Catalase phenotype from whole bacterial genomes
(protein sequences)
tags:
- biology
- bacteria
- bacformer
- prokaryotes
- genomic
- genome
- protein
size_categories:
- 1K<n<10K
Dataset for predicting Catalase phenotype from whole bacterial genomes (protein sequences)
A dataset of over 1k bacterial genomes across species with the Catalase as label. Catalase denotes whether a bacterium produces the catalase enzyme that breaks down hydrogen peroxide (H₂O₂) into water and oxygen, thereby protecting the cell from oxidative stress. Here, we provide binary Catalase labels, therefore the problem is a binary classification problem.
The genome protein sequences have been extracted from GenBank. Each row contains a list of protein sequences present in the bacterial genome, ordered by their location on the chromosome and plasmids.
The phenotypic traits have been extracted from [1].
Usage
Please see the Finetuning Bacformer for phenotypic traits prediction tutorial for an example on how to use the dataset.
References
[1] Weimann, Aaron, et al. "From genomes to phenotypes: Traitar, the microbial trait analyzer." MSystems 1.6 (2016): 10-1128.