Jnicol has created an app/bot to iterate thorugh permutations of nucloetides to solve eteRNA shapes. I am proposing additional codes for to reduce iterations based on eteRNA hot-keys.
Application/Bot: Bot for solving rna designs v0.2
Located at: http://www.amelior.com/bot.html
Author: jnicol (john)
Recap: Runs permutations of possible nucleotides in an RNA sequence based on input of control codes: base or modified dot-bracket code of target shape
Definitions and behaviors
(1) Seeking behavior: runs permutations. Application/bot will try different control codes to specify among the available RNA nucleotides specified
Nucleotides in Pairs
Current control codes [from base dot-bracket code]:
( 1st nucleotide of a pair that can be first nucleotide of these 6 choices: Au, Ua, Ug, Gu, Gc, or Cg
) 2nd nucleotide of a pair that can be any matching nucleotide that pairs with specific 1st nucleotide among Au, Ua, Ug, Gu, Gc, or Cg
Proposed additional control codes [blend of dot-bracket code and eteRNA hot-key equivalents for]:
Q 1st nucleotide of a pair that can be first nucleotide of these 2 choices: Au, Ua
q 2nd nucleotide of a pair that can be any matching nucleotide that pairs with specific 1st nucleotide among Au, Ua
W 1st nucleotide of a pair that can be first nucleotide of these 2 choices: Ug, Gu
w 2nd nucleotide of a pair that can be any matching nucleotide that pairs with specific 1st nucleotide among Ug, Gu
E 1st nucleotide of a pair that can be first nucleotide of these 2 choices: Gc, or Cg
e 2nd nucleotide of a pair that can be any matching nucleotide that pairs with specific 1st nucleotide among Gc, or Cg
Unpaired Nucleotides – control code [from base dot-bracket code]:
. an unpaired nucleotide that can be any of A, U, G or C
(2) Fully specified/no permutations. Application/bot will use only the nucleotide specified
Nucleotides in Pairs [blend of dot-bracket code and standard letter abbreviations]:
A Adenine as 1st nucleotide of bonded pair
a Adenine as 2nd nucleotide of bonded pair
U Urasil as 1st nucleotide of bonded pair
u Urasil as 2nd nucleotide of bonded pair
G Guanine as 1st nucleotide of bonded pair
g Guanine as 2nd nucleotide of bonded pair
C Cytosine as 1st nucleotide of bonded pair
c Cytosine as 2nd nucleotide of bonded pair
Unpaired Nucleotides [blend of dot-bracket code and eteRNA hot-key equivalents for]:
1 Adenine
2 Uracil
3 Guanine
4 Cytosine