Sampling and Bias in Degenerate Codon Protein Libraries
Ensembles of protein variants are widely used in enzyme engineering and ligand discovery. A common strategy for library generation involves degenerate codons at specific sites within scaffolds or as standalone peptides. But such schemes often create uneven abundances of library members, especially as multiple randomized sites are introduced. To balance the need for complex libraries with practical limits of screening systems, we present tools to address sampling statistics and bias for both library planning and downstream analysis.