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

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