Update README.md

README.md

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   - split: original
     path: data/original-*
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+# Dataset Card for 2025-scaffold-structures
+
+This dataset contains sequences from **aedupuga/scaffold-dataset** analysed to generate their MFE strucutre and energy and other strucutral features.
+
+## Dataset Details
+
+### Dataset Description
+- **Curated by:** Anuhya Edupuganti  
+- **Source:** www.addgene.org
+- **Processing:** www.nupack.org
+- **Dataset Overview:** - Each record represents a plasmid sequence with GC/AT content, predicted MFE structure and energy, and key structural features (base pairs, stems, hairpins, internal loops).
+
+### NUPACK-Friendly Sequence Mapping
+All IUPAC ambiguous nucleotides are mapped to representative bases for NUPACK folding predictions:
+
+| IUPAC Code | Meaning         | Representative Base |
+|------------|----------------|------------------|
+| A          | Adenine        | A                |
+| T          | Thymine        | T                |
+| G          | Guanine        | G                |
+| C          | Cytosine       | C                |
+| M          | A or C         | A                |
+| R          | A or G         | A                |
+| Y          | C or T         | C                |
+| W          | A or T         | A                |
+| S          | G or C         | G                |
+| K          | G or T         | G                |
+| H          | A, C, or T     | A                |
+| B          | C, G, or T     | C                |
+| V          | A, C, or G     | A                |
+| D          | A, G, or T     | A                |
+| N          | Any base       | A                |
+
+## Uses
+
+This dataset was developed as part of a class project to practice dataset construction.
+
+## Dataset Structure
+
+Each record in the dataset represents a single plasmid and contains the following fields:
+
+| Field Name           | Type     | Description |
+|---------------------|---------|-------------|
+| `sequence`          | string  | DNA sequence of the plasmid |
+| `length_bp`         | int64   | Total length of the plasmid in base pairs |
+| `GC_content`        | float64 | GC content of the plasmid sequence (%) |
+| `AT_content`        | float64 | AT content of the plasmid sequence (%) |
+| `nupack_sequence`   | string  | DNA sequence converted to NUPACK-compatible sequence using IUPAC representative base mapping |
+| `mfe_structure`     | string  | Minimum free energy (MFE) dot-bracket structure predicted using NUPACK |
+| `mfe_energy`        | float64 | MFE of the structure (kcal/mol) predicted using NUPACK |
+| `num_pairs`         | int64   | Number of base pairs in the predicted structure |
+| `stem_len_mean`     | float64 | Mean stem length in base pairs |
+| `num_stems`         | int64   | Total number of stems |
+| `num_hairpins`      | int64   | Number of hairpin loops |
+| `num_internal_loops`| int64   | Number of internal loops |
+
+## Dataset Creation
+
+### Source Data
+
+This dataset was derived from publicly available plasmid GenBank files.
+
+#### Data Collection and Processing
+
+- **Data Source:** Plasmid GenBank files downloaded from addgene.org  
+- **Selection Criteria:** Plasmids were selected based on relevance to synthetic biology applications, including scaffolds, reporter plasmids, and commonly used cloning backbones  
+- **Processing Steps:**  
+  1. Downloaded `.gbk` files corresponding to specific plasmid IDs  
+  2. Extracted sequence information, plasmid length, and functional annotations  
+  3. Calculated GC and AT content  
+  4. Converted sequences to **NUPACK-compatible sequences** using IUPAC representative base mapping  
+  5. Predicted minimum free energy (MFE) secondary structures using **NUPACK**  
+  6. Extracted structural features: `num_pairs`, `stem_len_mean`, `num_stems`, `num_hairpins`, `num_internal_loops`  
+
+## Dataset Card Contact
+
+Anuhya Edupuganti: aedupuga@andrew.cmu.edu