research-clotho 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.

Click to visit the official Merlin site.

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


  • Coming soon!

Accessing Merlin

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

Try Merlin

Recent news stories for Merlin

CIDAR Project Lead

Michael Quintin

Michael Quintin

CIDAR Collaborators

Swapnil Bhatia, PhD


  • S. D. D. Ahmed Samir and Bhatia, Merlin: a software framework for mage, 2012.
    author = {Ahmed, Samir and Bhatia, Swapnil and Densmore, Douglas},
    title = {Merlin: a software framework for MAGE},
    howpublished = {talk presented at SynBERC Spring Retreat, University of California-Berkeley},
    month = {March},
    year = {2012},
    keywords = {synthetic biology},
    timestamp = {2013.08.13}

  • M. J. Quintin, N. J. Ma, S. Ahmed, S. Bhatia, A. Lewis, F. J. Isaacs, and D. Densmore, “Merlin: computer-aided oligonucleotide design for large scale genome engineering with mage,” Acs synthetic biology, iss. ja, p. null, 2016. doi:10.1021/acssynbio.5b00219
    [BibTeX] [Download PDF]
    author = {Michael James Quintin and Natalie Jing Ma and Samir Ahmed and Swapnil Bhatia and Aaron Lewis and Farren J. Isaacs and Douglas Densmore},
    title = {Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE},
    journal = {ACS Synthetic Biology},
    year = {2016},
    volume = {0},
    number = {ja},
    pages = {null},
    note = {PMID: 27054880},
    doi = {10.1021/acssynbio.5b00219},
    eprint = { },
    url = {