pLOT Plasmid Plotter Manual

Download the current version of the pLOT installation file.

1. Introduction
2. Getting Started
   • Download the pLOT installation file
   • Installing pLOT
   • Checking for updates
3. Main window components
   • Main Window Components
   • The Tools Docking Window
   • The Feature Viewer Docking Window
4. Creating and Editing Projects
   • Creating a new sequence
   • Opening an existing file
   • Saving your sequence
   • Annotating your sequence manually
   • Setting the Project's Codon Table
5. Sequence Manipulations
   • Inserting sequences
   • Deleting sequences
   • Rotating a sequence
   • Reverse/complementing a sequence
6. Feature Annotations
   • Annotation properties
   • Creating a new annotation
   • Editing annotations
   • Setting a feature's map graphic
   • Setting feature graphic drawing orders
   • Setting a feature's codon table
   • Editing a feature's references
   • Changing a feature’s sequence to case to uppercase or lowercase
7. Annotation 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
     • Editing annotation properties
     • Removing of duplicate entries
     • Using categories
   • Auto-annotation of a sequence
8. Restriction Analysis
   • Selecting individual enzymes
   • Setting up multi-enzyme mixes
   • Adding new enzymes to the database (not yet implemented)
9. Tools
   • Converting Uppercase to Exons
     • Example using NRF1
   • DNA Element Search
   • Converting Base Pair position to codon number
   • Converting codon number to Base Pair position
   • Converting an amino acid sequence to a DNA sequence
10. Virtual Gel Electrophoresis
    • Opening the Virtual Gel Window
    • Setting the minimum fragment size
    • Show/Hide band sizes
    • Identifying the band in your sequence
    • Selecting ladders
    • Adding or editing ladders
11. 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.