joeyisgoed/codon-optimizer

Codon Optimizer

Multi-objective codon optimization tool based on the GenScript GenSmart algorithm (Patent WO2020024917A1).

Features

• —NSGA-III Optimization: Uses multi-objective genetic algorithm for comprehensive optimization
• —Three Optimization Indices:
• —Harmony Index: Match codon usage to highly-expressed genes
• —Codon Context Index: Optimize codon pair preferences
• —Outlier Index: Minimize adverse sequence features (GC content, repeats, motifs)
• —10 Expression Hosts: E. coli, Human, CHO, Yeast, Mouse, Insect, and more
• —Restriction Site Exclusion: Avoid common restriction enzyme cut sites
• —Comprehensive Metrics: CAI, GC content, and optimization indices

Usage

1. 1.Paste your protein or DNA sequence
2. 2.Select target expression organism
3. 3.Optionally select restriction sites to exclude
4. 4.Click "Optimize Sequence"
5. 5.Copy the optimized DNA sequence

Algorithm

The optimization algorithm is based on GenScript's patent WO2020024917A1, which describes:

1. 1.Harmony Index (H): Measures codon usage frequency match to reference highly-expressed genes
2. 2.Codon Context Index (CC): Evaluates codon pair placement optimization
3. 3.Outlier Index (OI): Penalizes adverse features like extreme GC content, repeats, and splice sites

The NSGA-III algorithm optimizes all three objectives simultaneously to find Pareto-optimal solutions.

References

• —GenScript GenSmart Codon Optimization
• —Patent WO2020024917A1
• —Deb, K., & Jain, H. (2014). An evolutionary many-objective optimization algorithm using reference-point-based nondominated sorting approach. IEEE TEVC.