Update README.md

README.md

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----
-license: mit
----
+---
+license: mit
+tags:
+- biology
+- protien-sequences
+- dna-database
+- raw-fasta
+- dna
+size_categories:
+- 10M<n<100M
+---
+
+## DNA Sequence Database from NCBI
+
+Welcome to the curated DNA sequence dataset, automatically gathered from NCBI using the Enigma2 pipeline. This repository provides ready-to-use CSV and Parquet files for downstream machine-learning and bioinformatics tasks.
+
+## 📋 Dataset Overview
+
+* **Scope**
+
+  * A collection of topic-specific DNA sequence sets (e.g., BRCA1, TP53, CFTR) sourced directly from NCBI’s Nucleotide database.
+* **Curation Process**
+
+  1. **Query Design**
+
+     * Predefined Entrez queries (gene names, organism filters) identify relevant GenBank records.
+  2. **Batch Retrieval**
+
+     * Sequences fetched in controlled batches to respect rate limits and ensure reliability.
+  3. **Quality Control & Filtering**
+
+     * Records shorter than 100 bp or exhibiting parsing errors were omitted.
+  4. **Metadata Extraction**
+
+     * For each sequence, we record:
+
+       * **ID** (accession number)
+       * **Name** (full FASTA description)
+       * **Length** (base-pair count)
+  5. **Export**
+
+     * Data saved in both CSV and Parquet formats for seamless integration with Python, R, and big-data frameworks.
+
+## 📂 Dataset Structure
+
+Each topic is stored in its own file under the `datasets/` directory:
+
+```
+datasets/
+├── BRCA1_Gene_AND_Homo_sapiens_Organism.csv
+├── BRCA1_Gene_AND_Homo_sapiens_Organism.parquet
+├── TP53_Gene_AND_Homo_sapiens_Organism.csv
+├── TP53_Gene_AND_Homo_sapiens_Organism.parquet
+…  
+```
+
+**File contents** (4 columns):
+
+| Column     | Description                                    |
+| ---------- | ---------------------------------------------- |
+| `id`       | NCBI accession ID                              |
+| `name`     | Full FASTA-style description                   |
+| `length`   | Original sequence length (in base pairs)       |
+| `sequence` | Raw DNA string (A/C/G/T; no alignment padding) |
+
+## 🚀 How to Use
+
+```python
+from enigma2 import Database, EntrezQueries, convert_fasta
+
+queries = EntrezQueries()  # contains about 20 queries
+db = Database(topics=queries(), out_dir="./data/", mode='csv', email="[email protected]", retmax=500, max_rate=10, raw=True)
+db.build_raw()
+
+# inspect first record
+print(ds[0])
+# → {'id': 'NM_007294.3', 'name': 'Homo sapiens BRCA1 transcript …', 'length': 1863, 'sequence': 'ATGGATT…'}
+```
+
+Or, in a Unix shell:
+
+```bash
+pip install datasets
+datasets-cli download -d shivendrra/dna-ncbi -s BRCA1_Gene_AND_Homo_sapiens_Organism.csv
+```
+
+## 🔍 Recommended Workflows
+
+* **Feature Engineering**: k-mer counting, GC content analysis
+* **Sequence Modeling**: RNNs, Transformers on raw DNA
+* **Phylogenetic Studies**: distance matrices from sequence distances
+
+## 🔗 Source Code
+
+The full data-gathering and processing pipeline is open-source:
+[Enigma2](https://github.com/shivendrra/enigma2)
+
+
+## 📖 Citation
+
+If you use this dataset in your work, please cite:
+
+```
+@misc{shivendrra_enigma2_2025,
+  author = {Shivendrra, Harsh and contributors},
+  title = {Enigma2 NCBI DNA Dataset},
+  year = {2025},
+  howpublished = {\\url{https://huggingface.co/datasets/shivendrra/EnigmaDataset}}
+}
+```
+
+## 📝 License
+
+This dataset is released under the [MIT License](LICENSE).
+Feel free to reuse and adapt—with attribution.