WheatConserve – Conserved Regions, SNP, and Primer Analysis for Wheat CDS

WheatConserve is an open-source, interactive bioinformatics tool for identifying conserved coding regions and SNP variations across multiple wheat (Triticum aestivum) cultivars using CDS sequences. It also enables automatic primer design and functional annotation via NCBI BLAST.

---

Key Features

• Upload multi-sequence FASTA files (CDS)
• Perform Multiple Sequence Alignment (MSA)
• Detect conserved regions based on user-defined thresholds
• Identify and filter SNPs (Single Nucleotide Polymorphisms)
• Design PCR primers around selected SNPs
• Visualize:
  • GC content
  • SNP distribution
  • Conserved region maps
• Annotate sequences via NCBI BLAST
• Export results as CSV, Excel, or PDF reports

---

Example Use Case

Given CDS sequences from multiple wheat cultivars, WheatConserve:

• Detects conserved coding regions
• Highlights sequence polymorphisms
• Designs primers suitable for genetic marker development
• Predicts potential gene/protein function using BLAST

This tool is ideal for wheat genomics researchers, plant molecular biologists, and bioinformatics educators.

---

How It Works

1. Upload a multi-FASTA file with cultivar-specific CDS.
2. The tool performs MSA and analyzes:
   • Conservation scores
   • SNP locations
   • GC content
3. Primer design is triggered for polymorphic regions.
4. Optional BLAST annotation provides functional insights.
5. Export summarized and visualized outputs.

---

Installation

git clone https://github.com/AHMEDY3DGENOME/WheatConserve.git
cd WheatConserve
pip install -r requirements.txt
streamlit run app.py

---

Input Format

Multi-sequence FASTA format with unique cultivar identifiers:

>cultivar_A
ATGC...
>cultivar_B
ATGT...
>cultivar_C
ATGC...

---

File Structure

├── app.py                  # Main Streamlit interface
├── modules/                # Core analysis modules
│   ├── alignment.py
│   ├── gc_content.py
│   ├── snp_analysis.py
│   ├── conserved.py
│   └── pdf_report.py
├── example_data/           # Example FASTA sequences
├── requirements.txt
└── README.md

---

Screenshots

🔹 Main Interface

🔹 Alignment Summary

🔹 SNP Analysis

🔹 SNP Distribution

🔹 Conserved Region Summary

🔹 Conserved Region Map

🔹 GC Content Analysis

🔹 Primer Design

🔹 BLAST Output

---

Live Demo

Try WheatConserve on Streamlit Cloud:
https://wheatconserve-mamebvqtw6ckefdcds7rcn.streamlit.app/

---

License

MIT License – Free to use, modify, and distribute.

---

Feedback & Contributions

Contributions, bug reports, and suggestions are welcome via GitHub Issues and Pull Requests.

---

Citation

If you use WheatConserve in your research, please cite:

@misc{wheatconserve2025,
  author       = {Ahmed Yassin},
  title        = {WheatConserve: Conserved Region and SNP Analysis Tool for Wheat CDS},
  year         = {2025},
  howpublished = {\url{https://github.com/AHMEDY3DGENOME/WheatConserve}},
  note         = {Open-source bioinformatics tool},
}