The iGEM and Addgene datasets used to characterize REPP are included in Supporting Information files.įunding: The funder (Lattice Automation, Inc.) provided support in the form of salaries for author J.T. Binaries and sequence repository files are available from SourceForge at. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: Source code is available from Github at. Received: SeptemAccepted: DecemPublished: January 9, 2020Ĭopyright: © 2020 Timmons, Densmore. PLoS ONE 15(1):Įditor: Ruslan Kalendar, University of Helsinki, FINLAND The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.Ĭitation: Timmons JJ, Densmore D (2020) Repository-based plasmid design. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly ®. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly.
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The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade.