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====== pLOT Plasmid Plotter Manual ======
Download the [[Downloads|current version]] of the pLOT installation file.
===== Table of Contents =====
  - [[Introduction|Introduction]]
  - [[Getting Started|Getting Started]]
    * [[Getting Started#Download the pLOT installation file|Download the pLOT installation file]]
    * [[Getting Started#Installing pLOT|Installing pLOT]]
    * [[Getting Started#Checking for updates|Checking for updates]]
  - [[Main window components and menu items|Main window components]]
    * [[Main window components and menu items#Main Window Components|Main Window Components]]
    * [[Main window components and menu items#The Tools Docking Window|The Tools Docking Window]]
    * [[Main window components and menu items#The Feature Viewer Docking Window|The Feature Viewer Docking Window]]
  - [[Creating and Editing Projects|Creating and Editing Projects]]
    * [[Creating and Editing Projects#Creating a new sequence|Creating a new sequence]]
    * [[Creating and Editing Projects#Opening an existing file|Opening an existing file]]
    * [[Creating and Editing Projects#Saving your sequence|Saving your sequence]]
    * [[Creating and Editing Projects#Annotating your sequence manually|Annotating your sequence manually]]
    * [[creating_and_editing_projects#Setting the Project Codon Table|Setting the Project's Codon Table]]
  - [[Sequence Manipulations|Sequence Manipulations]]
    * [[Sequence Manipulations#Inserting sequences|Inserting sequences]]
    * [[Sequence Manipulations#Deleting sequences|Deleting sequences]]
    * [[Sequence Manipulations#Rotating a Sequence|Rotating a sequence]]
    * [[Sequence Manipulations#Reverse/complementing a sequence|Reverse/complementing a sequence]]
  - [[Feature Annotations|Feature Annotations]]
    * [[Feature Annotations#Annotation properties|Annotation properties]]
    * [[Feature Annotations#Creating a new annotation|Creating a new annotation]]
    * [[Feature Annotations#Editing annotations|Editing annotations]]
    * Setting a feature's map graphic
    * Setting feature graphic drawing orders
    * Setting a feature's codon table
    * Editing a feature's references
    * [[Feature Annotations#Changing a feature’s sequence to case|Changing a feature’s sequence to case to uppercase or lowercase]]
  - [[Annotation Library|Annotation Library]]
    * [[annotation_library#Adding features from an existing sequence to the library|Adding features from an existing sequence to the library]]
      * [[Annotation Library#Adding individual annotations from a project to the library|Adding individual annotations from a project to the library]]
      * [[Annotation Library#Adding all Items from a project to the library|Adding all Items from a project to the library]]
    * [[annotation_library#Managing your annotation library|Managing your annotation library]]
      * [[Annotation Library#Editing annotation properties|Editing annotation properties]]
      * [[Annotation Library#Removing of duplicate entries|Removing of duplicate entries]]
      * [[Annotation Library#Using categories|Using categories]]
    * [[Annotation Library#Auto-annotation of a sequence|Auto-annotation of a sequence]]
  - [[Restriction Analysis|Restriction Analysis]]
    * [[Restriction Analysis#Selecting individual enzymes|Selecting individual enzymes]]
    * [[Restriction Analysis#Setting up multi-enzyme mixes|Setting up multi-enzyme mixes]]
    * [[Restriction Analysis#Adding new enzymes to the database|Adding new enzymes to the database]] (not yet implemented)
  - [[Tools|Tools]]
    * [[tools#Converting Uppercase to Exons|Converting Uppercase to Exons]]
      * [[Converting Uppercase to Exons Example|Example using NRF1]]
    * [[tools#DNA Element Search|DNA Element Search]]
    * [[tools#Converting Base Pair position to codon number|Converting Base Pair position to codon number]]
    * [[tools#Converting codon number to Base Pair position|Converting codon number to Base Pair position]]
    * [[tools#Converting an amino acid sequence to a DNA sequence|Converting an amino acid sequence to a DNA sequence]]
  - [[Virtual Gel Electrophoresis|Virtual Gel Electrophoresis]]
    * [[virtual_gel_electrophoresis#Opening the Virtual Gel Window|Opening the Virtual Gel Window]]
    * [[virtual_gel_electrophoresis#Setting the minimum fragment size|Setting the minimum fragment size]]
    * [[virtual_gel_electrophoresis#Show/Hide band sizes|Show/Hide band sizes]]
    * [[virtual_gel_electrophoresis#Identifying the band in your sequence|Identifying the band in your sequence]]
    * [[virtual_gel_electrophoresis#Selecting ladders|Selecting ladders]]
    * [[virtual_gel_electrophoresis#Adding or editing ladders|Adding or editing ladders]]
  - [[start#Disclaimer|Disclaimer]]

===== Disclaimer =====
  By using this program, you agree not to hold me responsible for any incidents of program crashes, inadvertent
  data loss, nuclear disasters or anything else that may happen as a result of use.