DNA Design for Large Scale Genome Engineering

Merlin is a web-based application for genomic reprogramming via a rapid and efficient method known as Multiplex Automated Genome Engineering (MAGE). This process can be used to target many regions on a genome simultaneously, in order to construct highly modified organisms, or to create diverse populations and explore a large genome landscape.

Merlin provides methods to generate a pool of single-stranded DNA oligos with which MAGE experiments can be carried out. These oligos are optimized not only for recombination efficiency, but also to minimize off-target interactions.

Merlin also provides methods to predict allelic replacement rates, in order to show how many MAGE cycles are necessary for an experiment.

Key Features

  • Generate an optimized set of ssDNA oligos for recombineering through MAGE

  • Predict and visualize allelic replacement efficiency to assist in experiment planning and validation


  • Merlin was funded by grants from the National Science Foundation, The National Institutes of Health, and the Gruber Foundation


Merlin is still in development, but you can access its features here:

Screen Shots