Copy and Paste Secondary Structure String

As well as copying the nucleotide sequence to the browser’s copy/paste buffer, I’d love to be able to easily copy and/or paste the current secondary structure string (target or MFE). So often in designing a puzzle of working with a lab it would be helpful to grab the current secondary structure (shape) to either save it for later or as an example in a text document or to grab the MFE shape and save it back as the target shape.


I agree. This would be very nice, with a one click button to grap the dot bracket. It will be a help too for those who work without side tools.

For now I can recommend a fine small script by Nando, that will dig up the dot bracket, when given an lab or puzzle ID. (It kills tails and such on lab puzzles, so one will still have to add details. But beats making the structure by hand in the puzzle maker.)…

Additional idea that would greatly speed up lab submissions. It would be helpful if I could simply grab the RNA sequence of a design, directly from the lab list. As of now I have to enter the design, when I right well know I want to make a mod of a past lab and just want the sequence for copying. But I guess, I can use Meechls and Omei’s spreadsheet for getting around that. (Big thx again, Meechl and Omei!)

Until recently, you could at least get the structure from one place or another in the UI that led up to the sequence browser screen. As far as I can tell, that capability is no longer to be found in the UI. :frowning:

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True. That was the target structure as well and sometimes what you want is the current MFE structure.

There are a couple difficulties that need to be properly taken care of if we are to implement such a tool. Designs have exactly one sequence, but possibly, N states.

The copy side of the problem: copy all structures in all modes and all states? only the states of the current target/native mode? what about the PIP mode? copy only the currently viewed state in whatever target/native mode it currently is?

The paste side of the equation: input validation, what should the applet do when receiving only one structure for a switch puzzle, which state is it? or reject that input?

And all of it has to stay intuitive and simple enough…

Also, I don’t really understand “grab the MFE shape and save it back as the target shape”, unless we’re talking about the puzzlemaker. Is that what you meant?

For starters I would work with one secondary structure at a time in non-PIP mode. You could do multiple lines for PIP mode I suppose.

And “grab the MFE shape and save it back as the target shape” is what I do in the Puzzle Maker, but it could also apply to an “Unlocked” mode (discussed elsewhere) for labs.

For the copy side, how about a pop-up window that had all the relevant structure strings, nicely labelled? The user could than cut the one(s) wanted.