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Prediction of RNA Secondary Structure by Energy Minimization

Michael Zuker

Institute for Biomedical Computing
Washington University, Campus Box 8036
700 S. Euclid Avenue
St. Louis, MO 63110

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• 1. Introduction
• 2. Materials - Computer Equipment and Programs
• 3. Methods 1 - Running the folding programs
  • 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
• 4. Methods 2 - Using special features
  • 4.1 Energy Parameter
  • 4.2 The ``Single force'' option
  • 4.3 The ``Double Force'' option
  • 4.4 The ``Closed Excision'' option
  • 4.5 The ``Open Excision'' option
  • 4.6 The ``Single Prohibit'' option
  • 4.7 The ``Double Prohibit'' option
  • 4.8 Remaining options
• 5. Methods 3 - Additional programs
  • 5.1 batgen - Command file generation for batch runs
  • 5.2 cttobp - Interconversion between ct files and region files
  • 5.3 The distance program
  • 5.4 Computing the energy of a folding
  • 5.5 Creating a ``hard copy'' of an energy dot plot
  • 5.6 Folding at different temperatures
  • 5.7 Drawing secondary structures
• 6. Notes
  • 6.1 Error messages in lrna and crna
    • 6.1.1 Traceback errors
    • 6.1.2 Printer output error
    • 6.1.3 Other errors
  • 6.2 Forcing base pairs
• Acknowledgements
• References
• About this document ...

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