However, pLannotate is intended primarily for annotating naturally occurring plasmids and not really built for annotating cloning vectors. It also displays a graphical map of the annotated plasmid, explains the provenance of each feature annotation, and allows results to be downloaded in a variety of formats. This web server allows users to quickly and comprehensively annotate plasmid features using large databases of genetic parts and proteins. Furthermore, the RF-cloning website is somewhat limited in its offerings as users cannot manipulate, re-color or re-render the plasmid map images or modify the sequence text in any substantive manner.Īnother plasmid annotation tool is pLannotate ( 6). While very convenient, this is not the way most cloning experiments are done. RF cloning is a PCR-based method that allows the insertion of essentially any sequence into any plasmid at any location without the need for restriction enzymes or ligation enzymes. However, RF-cloning is a very specialized web server designed to support RF cloning and the manipulation of RF-cloning plasmids only. This website has two sequence editors (one for the plasmid and one for the inserted gene) that supports customization and reformatting of the sequence display. This easy-to-use website allows users to paste in a plasmid sequence or select from about 40 popular RF plasmids, to choose an insert sequence and display a colorful, annotated plasmid map. One example of a web-enabled plasmid mapping/editing tool is Restriction Free (RF) Cloning or RF-Cloning, which was published in 2012 ( 5). Web technologies and web-based visualization tools have made web-enabled plasmid mappers and web-enabled plasmid editors feasible for quite some time. The requirement for downloadable programs to support plasmid mapping and editing appears to be mostly historical, if not inertial. There are also several freely available downloadable programs for plasmid editing/viewing including ApE ( 4), which operates on Windows, MacOS and Linux, pDRAW32 ( which is Windows 10 compatible and Serial Cloner ( ), which is compatible with MacOSX, Windows and Linux. These programs support a wide variety of plasmid display options, plasmid annotation tools and sophisticated plasmid editing function. Examples of commercial, stand-alone plasmid mapping/editing programs include SimVector (available at ), SnapGene Viewer (SnapGene®, available at SeqBuilder Pro (available at ) and Vector NTI (Invitrogen) ( 3). The majority of modern plasmid editing/mapping software tools are either stand-alone programs or part of larger commercial, downloadable, platform-specific software packages. Because of the size and complexity of plasmid molecules, it has long been essential to use specialized computer programs to help identify, locate, edit and analyze the plasmid sequence as well as specialized programs to generate and visualize the resulting maps ( 2). Nearly every practicing molecular biologist has probably generated or edited a plasmid map (or cloning vector map) to guide them through a cloning or plasmid manipulation experiment ( 1). The generation and editing of plasmid maps is one of the most frequently performed operations in all bioinformatics. All the plasmid images and textual displays are downloadable in multiple formats. 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. The graphics for PlasMapper 3.0 have also been substantially upgraded. 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. 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. This database can be searched by plasmid names, sequence features, restriction sites, preferred host organisms, and sequence length. 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). PlasMapper 3.0 is the successor to PlasMapper 2.0 and offers many features found only in commercial plasmid mapping/editing packages. Plasmid maps are used to plan, design, share and publish critical information about gene cloning experiments. PlasMapper 3.0 is a web server that allows users to generate, edit, annotate and interactively visualize publication quality plasmid maps.
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