PyVADesign: a Python-based cloning tool for one-step generation of large mutant libraries

Motivation The generation and analysis of diverse mutants of a protein is a powerful tool for understanding protein function. However, generating such mutants can be time-consuming, while the commercial option of buying a series of mutant plasmids can be expensive. In contrast, the insertion of a synthesized double stranded DNA (dsDNA) fragment into a plasmid is a fast and low-cost method to generate a large library of mutants with one or more point mutations, insertions, or deletions. Results To aid in the design of these DNA fragments we have developed PyVADesign: a Python package that makes the design and ordering of dsDNA fragments straight-forward and cost-effective. In PyVADesign, the mutations of interest are clustered in different cloning groups for efficient exchange into the target plasmid. Additionally, primers that prepare the target plasmid for insertion of the dsDNA fragment, as well as primers for sequencing, are automatically designed within the same program. Availability PyVADesign is open source and available at https://github.com/CDDLeiden/PyVADesign and archived via Zenodo (https://doi.org/10.5281/zenodo.15057525). Supplementary information Supplementary data are available at Bioinformatics online.