--- license: cc-by-4.0 configs: - config_name: default data_files: - split: train path: data/train-* dataset_info: features: - name: accession dtype: string - name: organism dtype: string - name: sequence dtype: string - name: introns list: - name: after dtype: string - name: before dtype: string - name: end dtype: int64 - name: gene dtype: string - name: sequence dtype: string - name: start dtype: int64 - name: exons list: - name: after dtype: string - name: before dtype: string - name: end dtype: int64 - name: gene dtype: string - name: sequence dtype: string - name: start dtype: int64 - name: proteins list: - name: end dtype: int64 - name: gene dtype: string - name: sequence dtype: string - name: start dtype: int64 splits: - name: train num_bytes: 11536678696 num_examples: 1677609 download_size: 5448417115 dataset_size: 11536678696 task_categories: - text-classification - token-classification - translation tags: - Exons - Introns - Proteins - DNA pretty_name: DNA Coding Regions size_categories: - 1M
  • `sequence`: only the nucleotide sequence of the intron
  • `start`, `end`: coordinates relative to the DNA sequence
  • `gene`: gene name when annotated
  • `before`, `after`: short flanking sequences
    • | | **exons** | `list` | List of exonic regions associated with this DNA sequence. Same structure as `introns`. | | **proteins** | `list` | List of coding sequences (CDS) translated to amino acid sequences, with: | --- ## Applications This dataset can be directly used for: * **DNA to protein translation modeling** * **Exon and Introns classification** * **Splicing prediction** * **Genomic representation learning** * **Bioinformatics-focused LLM pretraining (DAPT)** --- ## Loading Example ```python from datasets import load_dataset dataset = load_dataset("gu-dudi/DNA_coding_regions") print(dataset) print(dataset["train"][0]) ``` --- ## Dataset Metadata * **Source:** NCBI GenBank * **Processed with:** Biopython, Pandas, tqdm * **Maintainer:** [Gustavo Henrique Ferreira Cruz](https://huggingface.co/GustavoHCruz) * **License:** Open for research and educational use * **Format:** JSON Lines (UTF-8) --- ## Disclaimer on data completeness Not all genomic entries in this dataset contain every type of annotation (exons, introns, and proteins). While the GenBank records were filtered to include sequences annotated with "exon", "intron", and "CDS" feature keys, the underlying annotations in GenBank are not always deterministic or complete. Some sequences may include only exons or introns without corresponding protein-coding regions, or vice versa. This reflects the inherent variability and curation differences across submissions in the GenBank database. --- ### Citation If you use this dataset in your research, please cite: ```bibtex @misc{gustavo_henrique_ferreira_cruz_2025, author = {Gustavo Henrique Ferreira Cruz}, title = {DNA\_coding\_regions (Revision 16f4e3a)}, year = 2025, url = {https://huggingface.co/datasets/GustavoHCruz/DNA_coding_regions}, doi = {10.57967/hf/7238}, publisher = {Hugging Face} } ``` --- ### Version and Integrity * **Version:** 1.0 * **Total entries:** 1,677,609 * **Deduplication:** duplicates removed based on `(sequence, organism)` pair * **Strand normalization:** handled during extraction --- ### Notes * Coordinates (`start`, `end`) are **relative to the parent DNA sequence**. * `sequence` inside each **intron/exon** corresponds *only to that region* (not the full DNA). * Protein sequences are already **translated amino acid chains**, not nucleotide fragments. --- *Developed as part of the Master’s research project on DNA sequence understanding and translation using deep learning models.*