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aedupuga/2025-scaffold-strucutres

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 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… See the full description on the dataset page: https://huggingface.co/datasets/aedupuga/2025-scaffold-strucutres.

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Dataset Card

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:
—Downloaded .gbk files corresponding to specific plasmid IDs
—Extracted sequence information, plasmid length, and functional annotations
—Calculated GC and AT content
—Converted sequences to NUPACK-compatible sequences using IUPAC representative base mapping
—Predicted minimum free energy (MFE) secondary structures using NUPACK
—Extracted structural features: num_pairs, stem_len_mean, num_stems, num_hairpins, num_internal_loops

Dataset Card Contact

Anuhya Edupuganti: aedupuga@andrew.cmu.edu