A program designed by Calc4me to randomly generate valid secondary structures for EteRNA puzzles.
If you have a change that will improve this, you can either fork this and make the change yourself, or message me on EteRNA, and I'll see what I can do. Any suggestions are very much welcome, and any issues you find can be reported in the issues on github.
For an explanation of the paramaters, look at params.md, and to see some recommended intital values, see initvals.md.
More updates coming soon!
- Gen 1
- First generation, simple and very rigid.
- Generated very messy seqences because of ) spam.
- Gen 2
- Second generation, improved on Gen 1.
- More customizable, but still was messy over 30 nt.
- Gen 3
- Third generation, improved on Gen 2 w/ new logic.
- Mainly cleaned up generation and made it more stable in the 20-40 nt range.
- Gen 4
- Fourth generation, overhauled Gen 3.
- Improved customization and cleaned up generation to 50-60 nts (with well-tuned paramaters)
- Gen 5
- Fifth generation, improved on Gen 4.
- More customization and both cleaned up generation massively, to the point where 200 nts are good.
- Gen 6
- Sixth generation, cleaned up Gen 5.
- Added more explanation, and cleaned up code, and added more comments and better logic.
- Gen 7
- Seventh generation, cleaned up Gen 6.
- Added internal loops and a few other minor improvements
- Gen 8
- Eighth gen, improved Gen 7.
- More variance (has gone down, less internal loops, etc.), presets, multiloop forcing, and small changes.
- Gen 8.1
- Add more comments for readability
- Cleaned up the code and fixed some logic errors, and added full_debug
- Gen 9 (in development)
- JSON file for easier modification of constraints?
- EteRNA script?
- 4,5,...-multiloop forcing?
- Internal loop forcing?
- More presets?
- Better UI