Lib.fold() with molecule - Lib.foldm()

Feedback Feature Suggestions
1

I would like to request that a new function be added to the script library that
outputs the structure of a sequence with the molecule located at a specific
NT location. Similar to Lib.fold(sequence) -
a Lib.foldm(sequence,position) function.
It’s being calculated and outputted in the puzzles so it doesn’t have to be written from scratch, just have to find the right code to copy I would think.

1 Like
2

It is actually quite the contrary: there are so many obstacles, I don’t even know where to begin. Before I write a long essay with dozens of bullet points to explain why, could you please tell us what you intend to do with it? This way, we could restrict the conversation to the essential bits only.

3

Ok. Since it’s not easy I will do it manually. More work for me but that’s fine. It looks
like I have a month to play with old data before I can do more active labs. (Which actually could be a good thing.)
Thanks for getting back to me.

5

I’m willing to help if I can, but you won’t let me know what you need exactly… Ok, then I will only say that your proposal/request suffers from at least two major flaws:

  • there’s no room to specify a ligand concentration
  • a position-based ligand-binding algorithm is conceptually flawed for the reasons I exposed in https://getsatisfaction.com/eternagam… and consequently, I’m not sure we should keep using that system, which makes me less than motivated to implement and provide the function in the scripting interface. There are ways to simulate it though (I used that in the FMN mimics related scripts for instance).
6

I tried to download Shape Data from the Download shape data tab for
Lab Results “MiRNA Switch Lab Round 2” but all I see is title and sequence.
I would be looking for sequence/score at a minimum. Is this date somewhere else
or am I doing something incorrect?

8

The SHAPE data download is quite unlikely to work, since there is no SHAPE data for that lab.

The experimental results are included in the GoogleSheet and Excel file linked in the conclusions of http://eterna.cmu.edu/web/lab/5750156/

10

There it is. Thanks.