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Wishart DS, Ren L, Leong-Sit J, Saha S, Grant JR, Stothard P, Singh U, Kropielnicki A, Oler E, Peters H, Gautam V. PlasMapper 3.0-a web server for generating, editing, annotating and visualizing publication quality plasmid maps. Nucleic Acids Res 2023:7143233. [PMID: 37099365 DOI: 10.1093/nar/gkad276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/05/2023] [Indexed: 04/27/2023] Open
Abstract
PlasMapper 3.0 is a web server that allows users to generate, edit, annotate and interactively visualize publication quality plasmid maps. Plasmid maps are used to plan, design, share and publish critical information about gene cloning experiments. PlasMapper 3.0 is the successor to PlasMapper 2.0 and offers many features found only in commercial plasmid mapping/editing packages. PlasMapper 3.0 allows users to paste or upload plasmid sequences as input or to upload existing plasmid maps from its large database of >2000 pre-annotated plasmids (PlasMapDB). This database can be searched by plasmid names, sequence features, restriction sites, preferred host organisms, and sequence length. PlasMapper 3.0 also supports the annotation of new or never-before-seen plasmids using its own feature database that contains common promoters, terminators, regulatory sequences, replication origins, selectable markers and other features found in most cloning plasmids. PlasMapper 3.0 has several interactive sequence editors/viewers that allow users to select and view plasmid regions, insert genes, modify restriction sites or perform codon optimization. The graphics for PlasMapper 3.0 have also been substantially upgraded. It now offers an interactive, full-color plasmid viewer/editor that allows users to zoom, rotate, re-color, linearize, circularize, edit annotated features and modify plasmid images or labels to improve the esthetic qualities of their plasmid map and textual displays. All the plasmid images and textual displays are downloadable in multiple formats. PlasMapper 3.0 is available online at https://plasmapper.ca.
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Affiliation(s)
- David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Leah Ren
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Jacques Leong-Sit
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sukanta Saha
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - Jason R Grant
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Paul Stothard
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Upasana Singh
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Abby Kropielnicki
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Eponine Oler
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Harrison Peters
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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