# reducing permutations in botsolver with added control codes **URL:** https://forum.eternagame.org/t/reducing-permutations-in-botsolver-with-added-control-codes/2152 **Category:** Tools **Created:** [June 8, 2014, 1:03am UTC](https://forum.eternagame.org/t/reducing-permutations-in-botsolver-with-added-control-codes/2152 "2014-06-08T01:03:00Z") **Posts on this page:** 1 **Page:** 1
### Author: ![lroppy](https://forum.eternagame.org/letter_avatar_proxy/v4/letter/l/8baadc/32.png) [@lroppy](https://forum.eternagame.org/u/lroppy) #### Post date: [June 8, 2014, 1:03am UTC](https://forum.eternagame.org/t/reducing-permutations-in-botsolver-with-added-control-codes/2152/1 "2014-06-08T01:03:00Z")
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](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