mogam-ai/CDS-BART-fungal-expression

📊 Fungal protein dataset

This dataset is a collection of RNA-seq data from a wide range of fungal species. Predicted expression level of protein-coding and tRNA genes from 459 species sampled from six out of the eight recognized fungal phyla. The original dataset is from CodonBERT.

⁉️ Dataset Contents

• Sequence: The mRNA sequence of the Fungal.
• Expression: The measured protein expression level.

🎯 Purpose

This dataset serves as a benchmark for fine-tuning models on a regression task, predicting expression behavior from its sequence. We used this dataset to fine-tune CDS-BART, a BART-based foundation model trained on massive mRNA sequences. Demonstrating its ability to perform downstream tasks related to mRNA regulation which are fine-tuned for various mRNA-related downstream task. CDS-BART available at GitHub

🔧Usage

from datasets import load_dataset

dataset = load_dataset('mogam-ai/CDS-BART-fungal-expression')

📚 Dataset Reference

Wint R, Salamov A, Grigoriev IV. Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution, Molecular Biology and Evolution (2022):39. Li, Sizhen, et al. "CodonBERT large language model for mRNA vaccines." Genome research 34.7 (2024): 1027-1035.