Just a few quick notes in reference to last week’s chat between the developers and the players.
Tentatively, we are planning on having chats between developers and players every other week. This means our next meeting will likely be on Wednesday, November 14, at 3:00 pm PST. We will confirm that soon - and looking forward to it!
As mentioned, the EteRNA team is planning on revising the scoring function for switch puzzles. While the new rules are not finalized yet, we feel that our current scoring scheme is a bit too harsh - we think that the new scoring system will be more fair AND generally result in higher scores for designs that correctly form the FMN aptamer. Look for an update on that within a week or so - no word yet on whether or not old puzzles will be re-scored.
We also mentioned that we are are pursuing other ligand-binding aptamers to drive RNA switches. We will start by focusing on the molecule theophylline - just like with FMN, there is a tight-binding aptamer for theophylline that we can plug into lots of different structures. For now, and the near future, we will mostly still work on FMN in the lab; theophylline puzzles will be restricted to the challenge section. One day, they will become lab puzzles, though!
"The procedure defined…was implemented using the scripting language Perl. This allows easy modifications…
On the other hand, the program makes use of the C routines of the Vienna RNA Package (via a Perl extension module)
, and thus has access to fast routines for computation of RNA secondary structures and base-pairing probabilities.
For the small example [33-nt]…the program takes about 1.3 s per sequence on a 333 MHz Pentium II.
While manual design is not too hard for such an example, the optimization procedure yields significantly
better sequences. For the 115-nt SV11 example…it designs one sequence in about 10 min."
So, a 3 GHz dual or quad processor should do our switch labs in 15-60 seconds by my estimation.
