GustavoHCruz/DNA_coding_regions

DNA Coding Regions Dataset

This is a curated collection of genomic sequences extracted directly from NCBI GenBank, designed to support research in introns and exons classification, DNA-to-protein translation, gene structure analysis, and biological sequence modeling with deep learning architectures.

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Source and Extraction Pipeline

All records were extracted from GenBank using Biopython.
The dataset construction followed a reproducible data processing pipeline written in Python, which:

• Downloads and parses GenBank records.
• Extracts genomic DNA sequences, their associated exons, introns, and coding sequences (CDS).
• Processes the strand orientation to produce normalized sequences.
• Removes duplicate entries based on (sequence, organism) pairs.
• Assembles each record into a structured JSONL format suitable for machine learning models.

The GenBank search query used for data collection was:

"genomic DNA"[Filter]
AND ("exon"[Feature Key] OR "intron"[Feature Key])
AND "CDS"[Feature Key]
AND ("3"[SLEN] : "16384"[SLEN])

You can find more information about the pipeline in the GitHub from the DNA Coding Regions repository.

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Dataset Structure

Each entry in the dataset corresponds to a unique DNA sequence, identified by its GenBank accession.
The dataset is serialized in JSON Lines (.jsonl) format and can be loaded with the Hugging Face datasets library.

Example record

{
  "accession": "NC_045512.2",
  "organism": "Homo sapiens",
  "sequence": "ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGAT...",
  "introns": [
    {
      "sequence": "TTGTAGACCAGTGCAGTA...",
      "start": 1450,
      "end": 1783,
      "gene": "ORF1ab",
      "before": "ATGCCDG",
      "after": "TAACAFG"
    }
  ],
  "exons": [
    {
      "sequence": "ATGGACACAAGTCAGG...",
      "start": 1,
      "end": 1449,
      "gene": "ORF1ab",
      "before": null,
      "after": "GT"
    }
  ],
  "proteins": [
    {
      "sequence": "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVL...",
      "start": 1,
      "end": 4405,
      "gene": "ORF1ab"
    }
  ]
}

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Field Descriptions

Field	Type	Description
accession	str	GenBank accession number for the DNA sequence.
organism	str	Name of the organism from which the sequence was derived.
sequence	str	The full genomic DNA sequence (processed strand).
introns	list	List of intronic regions associated with this DNA sequence. Each item contains: 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: sequence: protein sequence start, end: coordinates in the DNA sequence gene: gene name

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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)

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Loading Example

from datasets import load_dataset

dataset = load_dataset("GustavoHCruz/DNA_coding_regions")

print(dataset)
print(dataset["train"][0])

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Dataset Metadata

• Source: NCBI GenBank
• Processed with: Biopython, Pandas, tqdm
• Maintainer: Gustavo Henrique Ferreira Cruz
• License: Open for research and educational use
• Format: JSON Lines (UTF-8)

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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.

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Citation

If you use this dataset in your research, please cite:

@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}
}

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Version and Integrity

• Version: 1.0
• Total entries: 1,677,609
• Deduplication: duplicates removed based on (sequence, organism) pair
• Strand normalization: handled during extraction

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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.

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Developed as part of the Master’s research project on DNA sequence understanding and translation using deep learning models.