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codon-usage

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Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences. Use when scoring a gene's codon bias against a host, optimizing a CDS for heterologous expression, or studying synonymous codon selection.

When to use

• Analyze codon usage
• Score this gene against a host
• Optimize codons for expression
• Calculate CAI
• Calculate RSCU
• Calculate Nc
• Produce naive max-CAI codon-optimized sequences
• Studying synonymous codon selection

When not to use

• Final design for expression
• Considering translation ramp
• Considering 5' mRNA structure
• Considering GC extremes
• Considering cryptic regulatory elements
• Considering codon-pair bias

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