primer-designer-byao 0.1.0

An automated primer design pipeline for conserved regions with specificity validation

Primer Designer

An automated bioinformatics pipeline for designing PCR primers targeting conserved genomic regions with built-in specificity validation.

Features

• Automated Workflow: Integrates BLAST, MAFFT, and Primer3 into a seamless pipeline
• Conservation Analysis: Identifies conserved regions across homologous sequences
• Specificity Validation: Verifies primer specificity against NCBI databases
• Graphical Interface: User-friendly PyQt6 GUI for easy operation
• Command-Line Tools: Flexible CLI for batch processing and automation
• Configurable Parameters: Extensive customization via YAML configuration

Quick Start

Installation

# Step 1: Install Python package
pip install -e .

# Step 2: Set up bioinformatics tools (optional - automatic via Snakemake)
python setup_envs.py

Important: MAFFT and Primer3 are automatically installed when using Snakemake or the GUI. Manual setup is only needed if you want to use CLI tools directly. See INSTALL.md for details.

Launch GUI (Recommended for Beginners)

primer-designer

The GUI handles all dependencies automatically through Snakemake.

Run Pipeline via Snakemake

# First run: automatically creates Conda environments (may take 5-10 min)
snakemake --use-conda --conda-prefix ./envs -j 8

# Subsequent runs: fast execution using cached environments
snakemake --use-conda --conda-prefix ./envs -j 8 all

Workflow Overview

1. Remote BLAST: Query NCBI to find homologous sequences
2. MAFFT Alignment: Align sequences and identify conserved regions
3. Primer3 Design: Design primers targeting conserved areas
4. Specificity Check: Validate primers against off-target binding

Command-Line Tools

After installation, the following commands are available:

• primer-designer or primer-designer-gui - Launch graphical interface
• primer-blast - Run remote BLAST search
• primer-mafft - Perform MAFFT alignment and conservation analysis
• primer-design - Design primers using Primer3
• primer-specificity - Check primer specificity

Configuration

Edit config.yaml to customize:

• NCBI email and API key
• BLAST parameters (database, e-value, hit list size)
• Conservation detection thresholds
• Primer design constraints (Tm, GC%, size)
• Specificity checking parameters

Input Files

Place your FASTA files in backend/tasks/fastas/ or configure paths in config.yaml.

Output Files

• blast/*.xml - BLAST results in XML format
• mafft/*.bed - Conserved regions in BED format
• mafft/*.fasta - Multiple sequence alignments
• primer/*.tsv - Designed primer pairs
• primer/*_specificity.tsv - Specificity validation results

Requirements

• Python 3.8+
• Conda (for bioinformatics tools)
• 4 GB RAM minimum (8 GB recommended)

Documentation

• Installation Guide - Detailed setup instructions
• Configuration - Parameter reference

License

MIT License - see LICENSE file for details.

Citation

If you use this software in your research, please cite:

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