ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries

Abstract

Directed evolution has greatly facilitated protein engineering and provided new insights into protein structure—function relationships. DNA shuffling using restriction enzymes is a particularly simple and cost-effective means of recombinatorial evolution that is well within the capability of most molecular biologists, but tools for the design and analysis of such experiments are limited. Here we introduce a suite of freely available online tools to make the construction and analysis of chimeric libraries readily accessible to the novice. REcut (http://qpmf.rx.umaryland.edu/REcut.html) facilitates the choice of DNA fragmentation strategy, while Xover (http://qpmf.rx.umaryland.edu/Xover.html) analyzes chimeric mutants to reveal recombination patterns and extract quantitative data.

Keywords

• crossover
• directed evolution
• DNA shuffling
• recombination
• restriction enzyme
• chimera