PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment

Qi Wang, Bryce Kille, Tian Rui Liu, R. A. Leo Elworth and Todd J. Treangen ()
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Qi Wang: Rice University
Bryce Kille: Rice University
Tian Rui Liu: Rice University
R. A. Leo Elworth: Rice University
Todd J. Treangen: Rice University

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract With advances in synthetic biology and genome engineering comes a heightened awareness of potential misuse related to biosafety concerns. A recent study employed machine learning to identify the lab-of-origin of DNA sequences to help mitigate some of these concerns. Despite their promising results, this deep learning based approach had limited accuracy, was computationally expensive to train, and wasn’t able to provide the precise features that were used in its predictions. To address these shortcomings, we developed PlasmidHawk for lab-of-origin prediction. Compared to a machine learning approach, PlasmidHawk has higher prediction accuracy; PlasmidHawk can successfully predict unknown sequences’ depositing labs 76% of the time and 85% of the time the correct lab is in the top 10 candidates. In addition, PlasmidHawk can precisely single out the signature sub-sequences that are responsible for the lab-of-origin detection. In summary, PlasmidHawk represents an explainable and accurate tool for lab-of-origin prediction of synthetic plasmid sequences. PlasmidHawk is available at https://gitlab.com/treangenlab/plasmidhawk.git .

Date: 2021
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DOI: 10.1038/s41467-021-21180-w

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