We have a Pseudoknot Finder tool! Thank you jnicol for developing this great script for us!
After adding the Pseudoknot Finder script to your Favorites, open the OpenKnot lab puzzle and initiate the booster. The dialog box will pop up. Enter a title for the organism you are searching and a description such as the source (hyperlinks are supported), and paste the long sequence. Here is an mRNA I found on RNA Central.
Click the Apply button. The script will search 100-base segments at 20-base intervals, then return a list of pseudoknots found.
If desired, click on each Pseudoknot entry to view folding in Natural Mode. Once the player is comfortable with the tool, sequences can be submitted without reviewing each one. I’m keeping this one even though it has 6A in a row. Probably will synthesize and test fine. And if it doesn’t, not a big deal. We have plenty of slots.
I’m keeping this one as well even though it folds with the 5’ end. Only base 26 is involved.
If you want to delete a sequence from the list (not submit it), click Enabled to change to Disabled. Please note, any mutation made to the sequences in the list will not be saved when sequences are submitted. I asked jnicol to keep this tool very simple so that new players can learn it easily, no bells and whistles.
Click the Submit 6 designs button and designs will submit!
The script can process up to 500,000 bases, but a more manageable length RNA to search for pseudoknots is the 10,000 - 50,000 range. (To close the dialog box, click the script in the booster list again.)