http://www.plasmidplotter.com/wiki/ 2026-04-04T07:53:04+00:00 http://www.plasmidplotter.com/wiki/ http://www.plasmidplotter.com/wiki/lib/tpl/dokuwiki/images/favicon.ico text/html 2021-01-15T15:50:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=annotation_library&rev=1610725810&do=diff Go back to the pLOT Manual Table of Contents or Go to next Restriction Analysis The Annotations Library Adding features from an existing sequence to the library Adding individual annotations from a project to the library Adding all Items from a project to the library Managing your annotation library text/html 2021-01-15T15:01:28+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=checking_for_updates&rev=1610722888&do=diff Go back to the pLOT Manual Table of Contents Checking for Updates text/html 2021-01-18T13:10:17+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=converting_uppercase_to_exons_example&rev=1610975417&do=diff Go back to the pLOT Manual Table of Contents or Go back to Tools Converting Uppercase to Exons Example: NRF1 Some genome browser tools such as the UCSC Genome Browser allow you to download a genomic sequence and specify introns as lowercase. pLOT can use this to automate annotating of exons from sequences formatted in this manner. For example, to annotate the exons of NRF1: text/html 2021-01-19T13:01:17+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=creating_and_editing_projects&rev=1611061277&do=diff Go back to the pLOT Manual Table of Contents or Go to next Sequence Manipulations Creating a new sequence Opening an existing file Saving your sequence Annotating your sequence manually Setting the Project's Codon Table By default, projects assume that the standard codon table is used. A different codon table can be selected for the project by clicking the Tools menu, moving the mouse over the text/html 2021-01-15T15:00:18+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=download&rev=1610722818&do=diff Go back to the pLOT Manual Table of Contents pLOT Downloads Current version Change History text/html 2021-01-16T03:52:04+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=downloads&rev=1610769124&do=diff Go back to the pLOT Manual Table of Contents pLOT Downloads and Version History Current pLOT version Current Installation File Version: 1.0.18e Download Current Features Library Version: 1.0.1 Download Current Restriction Library Version: 1.0.0 Download Current Ladders Library Version: 1.0.0 text/html 2021-01-19T14:26:34+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=feature_annotations&rev=1611066394&do=diff Go back to the pLOT Manual Table of Contents or Go to next Annotation Library Feature Annotations Annotation properties Feature annotations have a number of properties that dictate how they appear on the map, their coordinates and orientation in the sequence and other. Feature annotations can be edited through any of the following ways: text/html 2021-01-19T14:34:31+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=feature_popup_menu&rev=1611066871&do=diff The Feature popup menu A right click on a feature on the map will display the Feature Popup Menu which allows for changes to the selected feature's properties. Submenus text/html 2021-01-16T03:26:03+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=getting_started&rev=1610767563&do=diff Go back to the pLOT Manual Table of Contents or Go to next Main Window Components and Menu Items Getting Started Download the pLOT installation file Download the current version of the pLOT installation file. Installing pLOT If you already have an installation, uninstall it. Open the Installation .Zip file and double click the “Setup.exe” file and then click OK. text/html 2021-01-15T14:59:59+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=installing_plot&rev=1610722799&do=diff Go back to the pLOT Manual Table of Contents Installing pLOT text/html 2021-01-15T15:47:12+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=introduction&rev=1610725632&do=diff Go back to the pLOT Manual Table of Contents or Go to next Getting Started Introduction Background pLOT is a molecular biology tool for mapping plasmids and manipulating sequences. It was initially intended only for my own personal use when I couldn't find software to do exactly what I wanted. Since I had used freeware plasmid editing software back in grad school, I decided to release this for free, noncommercial use in the hopes that it will help some poor grad student someday. pLOT can b… text/html 2021-01-18T16:27:40+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=main_window_components_and_menu_items&rev=1610987260&do=diff Go back to the pLOT Manual Table of Contents or Go to next Sequence Manipulations Main Window Components The main pLOT window consists of 4 parts. The Menu bar (Red), the Toolbar (Green) the Main map display (Light blue) and two detachable/docked windows. The Tools Docking Window The detachable Tools window's top panel can be used to edit the properties of the project such as the sequence name, source and organism as well as to open editors for project references and notes. text/html 2021-01-15T15:55:02+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=primers&rev=1610726102&do=diff Primers Using the Primer Library Adding Primers Manually Batch Removing Primers Editing Primers Saving the Library Toggling Primer Display By orientation By category text/html 2021-01-18T12:28:29+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=restriction_analysis&rev=1610972909&do=diff Go back to the pLOT Manual Table of Contents or Go to next Tools Restriction Analysis Selecting individual enzymes Setting up multi-enzyme mixes Adding new enzymes to the database (not yet implemented) text/html 2021-01-18T16:35:52+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=sequence_manipulations&rev=1610987752&do=diff Go back to the pLOT Manual Table of Contents or Go to next Feature Annotations Sequence Manipulations Inserting sequences Deleting sequences Rotating a Sequence Reverse/complementing a sequence text/html 2021-01-19T13:05:31+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=start&rev=1611061531&do=diff pLOT Plasmid Plotter Manual Download the current version of the pLOT installation file. Table of Contents * Introduction * Getting Started * Download the pLOT installation file * Installing pLOT * Checking for updates * Main window components * Main Window Components * The Tools Docking Window * The Feature Viewer Docking Window * Creating and Editing Projects * Creating a new sequence * Opening an existing file * Saving your sequence * Annotating your … text/html 2021-01-18T14:40:39+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=tools&rev=1610980839&do=diff Go back to the pLOT Manual Table of Contents or Go to next Virtual Gel Electrophoresis Tools Converting Uppercase to Exons Some genome browser tools such as the UCSC Genome Browser allow you to download a genomic sequence and specify introns as lowercase. pLOT can use this to automate annotating of exons from sequences formatted in this manner. See the text/html 2021-01-18T15:01:52+00:00 Anonymous (anonymous@undisclosed.example.com) http://www.plasmidplotter.com/wiki/doku.php?id=virtual_gel_electrophoresis&rev=1610982112&do=diff Go back to the pLOT Manual Table of Contents or Go to next Primers Opening the Virtual Gel Window When a project is loaded or started, the virtual gel can be shown by pressing (Ctrl + G) or clicking the Tools>Show Virtual Gel menu item. Setting the minimum fragment size