What is PROTÉGÉ PD?
PROTÉGÉ PD (PROTEin coding GEne for phylogenetic tag and identification - Primer Design) is a specialized tool for designing primers targeting protein-coding genes used in phylogenetic analysis and molecular identification. The tool implements the PhyloTag approach (Caro-Quintero, 2015), which focuses on identifying optimal primer sites in conserved protein-coding genes across multiple sequences.Key features
Phylogenetic primer design
Design primers optimized for phylogenetic analysis from multi-sequence alignments of protein-coding genes
Interactive visualization
Explore primer candidates through an interactive web interface with degeneracy and melting temperature analysis
Docker-based deployment
Run in an isolated environment with Python 3.10 and all dependencies pre-installed
Consensus-based selection
Automatically calculate consensus sequences and identify regions with configurable conservation thresholds
How it works
PROTÉGÉ PD follows a comprehensive workflow:Consensus calculation
A consensus sequence is generated based on your specified conservation percentage, with support for degenerate bases
Primer candidate identification
The tool scans the consensus for all possible primer positions based on codon length
Who should use PROTÉGÉ PD?
This tool is designed for:- Molecular biologists conducting phylogenetic studies using protein-coding genes
- Microbial ecologists developing molecular markers for taxonomic identification
- Researchers working with multi-sequence datasets who need to design consensus primers
- Scientists requiring primers with controlled degeneracy for broad taxonomic coverage
PROTÉGÉ PD is particularly useful when you need primers that amplify conserved regions across multiple related species or strains while maintaining phylogenetic resolution.
Next steps
Installation
Set up Docker and pull the PROTÉGÉ PD image
Quickstart
Run your first primer design analysis