SD-Muta (Site-Directed Mutagenesis Primer Generator)

Python tool for designing mutagenic primers for site-directed mutagenesis (SDM) using overlap extension PCR. Based on work of mds-mutagenesis

Features

• Automatic primer design - Generates tetrad primer combinations for SDM
• Species-specific codons - Uses codon preference tables for optimal expression
• Thermal analysis - Calculates Tm values and GC content for each primer
• Sorted output - Primers ranked by overlap Tm for easy selection

Quick Start

Installation

# Clone the repository
git clone <repo>

Usage

Basic usage:

python main.py data/examples/input_gene.txt data/examples/input_mutaa.txt Human

With custom output directory:

python main.py data/examples/input_gene.txt data/examples/input_mutaa.txt Human output/my_results

Input Files

Gene sequence file (input_gene.txt):

• DNA sequence in FASTA or plain text format
• Minimum length: 399 bps

Mutations file (input_mutaa.txt):

• One mutation per line
• Format: [Original_AA][Position][New_AA]
• Example: R147A, K123E, T862R

Supported Species

Ec, Yeast, Insect, Ce, Dm, Human, Mouse, Rat, Pig, Pp, At, Streptomyces, Zm, Tobacco, Sc, Cg

Output

Each mutation generates a file with primer pairs showing:

• Primer name - Mutation and orientation (5' or 3')
• Sequence - The oligonucleotide sequence
• Length - Number of bases
• GC - GC content percentage
• Tm - Melting temperature
• Overlap_Tm - Overlap region Tm for annealing

Requirements

• Python 3.7+
• BioPython (for sequence analysis)