SeqDelta

SeqDelta is an educational, exploratory bioinformatics tool for sequence-level mutation analysis. It compares a reference DNA FASTA sequence against a mutant DNA FASTA sequence, performs explicit pairwise alignment, separates nucleotide-level differences from codon and protein consequences, and exports the result as terminal output, standalone HTML, JSON, and CSV.

SeqDelta is intended for:

• classroom demos
• student portfolios
• exploratory sequence comparison
• lightweight local analysis workflows

It is not a clinical or diagnostic tool.

Features

• One-record FASTA input for reference and mutant sequences
• Global pairwise alignment
• Nucleotide-level mutation detection
• Codon-level consequence mapping
• Protein-level consequence comparison
• Effect classification for silent, missense, nonsense, frameshift, and in-frame indels
• CLI-first workflow with optional local web interface
• HTML, JSON, and CSV exports

Installation

Install the CLI directly from GitHub:

pip install git+https://github.com/milord-x/SeqDelta.git

Then run:

seqdelta compare reference.fasta mutant.fasta --html-report report.html

Download the Project

If you want the full repository locally:

git clone https://github.com/milord-x/SeqDelta.git
cd SeqDelta

Full Local Setup

If you want both the CLI and the local web app in a clean environment:

git clone https://github.com/milord-x/SeqDelta.git
cd SeqDelta
python -m venv .venv
source .venv/bin/activate
pip install -e .[dev]

Verify the install:

seqdelta --help
seqdelta compare --help
pytest

Quick Demo

seqdelta compare examples/reference.fasta examples/missense.fasta --html-report demo.html

CLI Usage

Basic comparison:

seqdelta compare reference.fasta mutant.fasta

Export all major formats:

seqdelta compare reference.fasta mutant.fasta --protein-view --json-out results.json --csv-out mutations.csv --html-report report.html

Current CLI options:

• --json-out
• --csv-out
• --html-report
• --protein-view
• --pretty/--plain

Local Web App

Run the local FastAPI app:

python app.py

Then open:

http://127.0.0.1:8000

The local web interface supports FASTA upload, browser-based result viewing, and downloadable HTML, JSON, and CSV outputs.

Example Data

Ready-to-run FASTA files are included in examples/:

• reference.fasta
• substitution.fasta
• missense.fasta
• silent.fasta
• frameshift.fasta

Development fixtures are kept in sample_data/.

Screenshots

The current recording shows the browser workflow end to end. Additional still screenshots can be added later for the upload page, results dashboard, mutation table, and alignment view.

Project Structure

SeqDelta/
├── app.py
├── cli.py
├── examples/
├── screenshots/
├── pyproject.toml
├── README.md
├── sample_data/
├── seqdelta/
├── static/
├── templates/
└── tests/

Limitations

• Assumes the coding frame starts at nucleotide position 1
• No CDS annotation or reading-frame offset input
• No transcript or exon awareness
• Codon consequence mapping is sequence-based
• Expects one FASTA record per file
• No HGVS normalization or clinical interpretation
• Not suitable for diagnostic or medical use

Positioning

SeqDelta should be presented as:

• an educational bioinformatics project
• an exploratory sequence analysis tool
• a sequence-level mutation comparison workflow

Development

Fallback local command:

python cli.py compare examples/reference.fasta examples/missense.fasta --html-report demo.html

Run tests:

pytest