Mutation Maker, An Open Source Oligo Design Platform for Protein Engineering

Abstract

Founded on principles of natural selection, directed evolution techniques harness high-throughput gene diversification methodologies to generate proteins with optimized properties for applications in research, therapeutic and industrial processes. However, design of gene libraries is typically hampered by scale and complexity, necessitating development of advanced automation and optimization tools that can improve efficiency and accuracy. At present, automated library design tools are obsolete, functionally limited or not freely available for commercial use. To address these issues, we developed Mutation Maker, an open source mutagenic oligo design software for large-scale protein engineering experiments. Mutation Maker is not only specifically tailored to multi-site random and directed mutagenesis protocols, but also pioneers bespoke mutagenic oligo design for de novo gene synthesis workflows. Enabled by a novel bundle of orchestrated heuristics, optimization, constraint-satisfaction and backtracking algorithms, Mutation Maker offers a versatile toolbox for gene diversification design at industrial scale. Supported by in-silico simulations and compelling experimental validation data, Mutation Maker oligos produce diverse gene libraries at high success rates irrespective of genes or vectors used. Finally, Mutation Maker was created as an extensible platform on the notion that directed evolution techniques will continue to evolve and revolutionize current and future-oriented applications.

Mutagenesis-Visualization: Analysis of Site-Saturation Mutagenesis Datasets in Python

“…A substantial number of software tools for different parts of the bioinformatics pipeline have been described in the literature. For the DNA library design, Mutation Maker and OneClick let users design oligos according to different specifications and much more (Tang et al 2012;Hiraga et al 2021). For the preprocessing of DNA reads, FLASH and PEAR tools merge pairedend reads, Cutadapt and trimmomatic remove adapter sequences (Zhang et al 2014;Bolger et al 2014) and QUASR provides a framework for the quantification and analysis of short reads (Gaidatzis et al 2015).…”