| --- |
| license: cc-by-4.0 |
| task_categories: |
| - feature-extraction |
| - table-to-text |
| tags: |
| - biology |
| - bioinformatics |
| - genomics |
| - protein-structure |
| - alphafold3 |
| - insect-science |
| pretty_name: InsectBase 3.0 Genomics and Protein Structures |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: "InsectBase_Genome/*" |
| --- |
| |
| # InsectBase 3.0: A Comprehensive Multi-omics Resource for Insects |
|
|
| [InsectBase](https://www.insect-genome.com/) is a specialized bioinformatics database providing extensive genomic and multi-omic resources for the insect research community. This repository hosts the high-throughput genomic sequences and predicted protein structures associated with the **InsectBase 3.0** update. |
|
|
| ## Dataset Description |
|
|
| - **Homepage:** [https://www.insect-genome.com/](https://www.insect-genome.com/) |
| - **Paper:** [Nucleic Acids Research (2025)](https://doi.org/10.1093/nar/gkaf1248) |
| - **Repository Contents:** |
| - `InsectBase_Genome/`: Large-scale insect genomic sequences (FASTA format). |
| - `InsectBase_Protein_Structure/`: High-confidence protein structures predicted via AlphaFold 3. |
|
|
| --- |
|
|
| ## 1. InsectBase_Genome |
| This subset contains the comprehensive insect genome assembly files in FASTA format. |
| |
| ### File Reconstruction |
| Due to the massive size of the genomic data (~400GB), the archive has been split into multiple chunks (7-10 parts) to ensure stable downloading. To reconstruct the original file, please use the following commands in your terminal: |
| |
| ```bash |
| # Navigate to the download folder |
| cd InsectBase_Genome |
|
|
| # Merge the split parts back into a single tar.gz file |
| cat InsectBase_genome.tar.gz.part* > InsectBase_genome.tar.gz |
|
|
| # Extract the FASTA files |
| tar -zxvf InsectBase_genome.tar.gz |
| |
| # (Optional) Verify integrity if sha256.txt is provided |
| sha256sum -c sha256.txt |
| ``` |
| |
| --- |
| |
| ## 2. InsectBase_Protein_Structure |
| This subset provides structural data for **29 specific gene families**. These structures were generated using **AlphaFold 3**, providing state-of-the-art accuracy for protein-insect physiological research and evolutionary analysis. |
| |
| - **Format:** `.pdb` or `.mmCIF` (compressed within family-specific archives). |
| - **Scope:** Covers major gene families critical to insect development, immunity, and metabolic processes. |
| |
| --- |
| |
| ## Citation |
| |
| If you use this dataset or the resources from InsectBase in your research, please cite the following paper published in *Nucleic Acids Research*: |
| |
| > Zuoqi Wang, Hao Chen, Shuo Jin, Zonghuan Li, Yang Mei, Yiqi Xiao, Chenfan Zhao, Tianyu Zhou, Fei Li, Ying Liu, Kang He, **InsectBase 3.0: a comprehensive multi-omics resource for insects**, *Nucleic Acids Research*, 2025;, gkaf1248, [https://doi.org/10.1093/nar/gkaf1248](https://doi.org/10.1093/nar/gkaf1248) |
| |
| --- |
| |
| ## Contact & Support |
| For more detailed information, interactive tools, and additional omics data (Transcriptomics, Metabolomics, etc.), please visit our official website: |
| **[https://www.insect-genome.com/](https://www.insect-genome.com/)** |
| |
| For technical issues regarding the data hosted on Hugging Face, please open an issue in this repository. |
| |
