PlasmidHawk: Alignment-based Lab-of-Origin Prediction of Synthetic Plasmids [article]

Qi Wang, Tian Rui Liu, R. A. Leo Elworth, Todd Treangen
2020 bioRxiv   pre-print
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, is computationally expensive to train, and wasn't able to provide the precise features that were used in its predictions. To address these
more » ... comings, we have 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 63% of the time and 80% 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 a novel, explainable, accurate tool for lab-of-origin prediction of synthetic plasmid sequences. PlasmidHawk is available at .
doi:10.1101/2020.05.22.110270 fatcat:go2fx62wozbgtfvs3stvk4ewfy