Their circuitous cloning histories often mean that present-day maps describing what features are found on plasmids are imprecise and missing information. Even now, when precision DNA synthesis and assembly methods are available, new plasmids typically incorporate pieces of existing plasmids. For decades, engineered plasmids were primarily constructed by combining chunks of naturally occurring DNA sequences using restriction enzymes or integrases. It has been nearly a half century since recombinant DNA technology was first developed and used to domesticate laboratory plasmids from their wild counterparts ( 1). The webserver for pLannotate is accessible at: Įngineered plasmids are widely used in the biological sciences for diverse applications that include amplifying DNA, overexpressing proteins, building genetic circuits and engineering metabolism. Finally, pLannotate displays a graphical map of the annotated plasmid, explains the provenance of each feature prediction, and allows results to be downloaded in a variety of formats. It employs a filtering algorithm to display only the most relevant feature matches and also reports feature fragments. pLannotate is powered by large databases of genetic parts and proteins. We created the open source pLannotate web server so users can quickly and comprehensively annotate plasmid features.
Existing plasmid annotation tools have limited feature libraries and do not detect incomplete fragments of features that are present in many plasmids for historical reasons and may impact their newly designed functions. Many engineered plasmids contain sequences-such as recombinant DNA from all domains of life, wholly synthetic DNA sequences, and engineered gene expression elements-that are not predicted by microbial genome annotation pipelines. Missing information about the presence, location, or precise identity of a plasmid feature can lead to unintended consequences or failed experiments. Since many plasmids contain DNA sequences that have been reused and remixed by researchers for decades, annotation of their functional elements is often incomplete. Engineered plasmids are widely used in the biological sciences.
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