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3. Methods 1 - Running the folding programs

Both lrna and crna can be run interactively. Menus are displayed and choices can be made regarding input and output. The first choice is run type.

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• 3.1 Run type selection
• 3.2 Output save file name selection
• 3.3 Run mode selection
• 3.4 Energy dot plot parameter selection
• 3.5 N best parameter selection
• 3.6 Input sequence file name selection
• 3.7 Input save file name selection
• 3.8 Energy file input
• 3.9 Output file and format selection
• 3.10 Main menu
• 3.11 Energy dot plot
  • 3.11.1 Changing the energy increment
  • 3.11.2 Selecting base pairs from the dot plot
  • 3.11.3 Computing structures
  • 3.11.4 Displaying the ``P-num plot''
  • 3.11.5 Choosing colors for the dot plot
  • 3.11.6 Creating a ``hard copy'' of the dot plot
  • 3.11.7 Final details in the dot plot

Michael Zuker
Thu Nov 2 14:28:14 CST 1995