Version Compatibility

Reference examples tested with: BioPython 1.83+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Codon Usage

Analyze codon usage patterns and calculate codon adaptation metrics using Biopython.

"Analyze codon usage" → Count codons in a coding sequence, compute frequencies and bias metrics.

• Python: Counter on 3-mers + CodonAdaptationIndex (BioPython)

"Optimize codons for expression" → Replace codons with host-preferred synonymous codons using a preference table.

• Python: custom mapping dict + Seq() (BioPython)