Using multiple criteria for evaluating mutations

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New ways of seeing what to mutate


As whbob said: The possible mutations in the e. coli ribosome is a larger number that stars in the Milky Way Galaxy. I welcome some constraints :)

Omei has shared some of his recent work: 

"I calculated a set of constraints for the 5S puzzle that is based solely on the degree of base conservation among gammaproteobacteria, which is the phylogenetic class that includes E coli."

Gammaprotobacteria 5s rrna sequence conservation in IUPAC


Basically he has compared the e. coli 5s rRNA with its closest relatives and used the IUPAC letter code to show what is is typically at a specific base position. 

This hints at which bases may be more likely to work for our 5s puzzle. 

aa

See Eternawiki

The constraint sequence itself: 

UGYYUGRYGRCMAUAGMRHDDUGGWMCCACCYGAYYCCAUBCCGAACUCRGHAGUGAAACGNHDYWKCGCCGAUGRUAGUGUGGSGHYUCSCCAUGYGARAGUAGGDMAYYGYCARRYWU


Coming multi color booster

Omei is currently plotting making a multi color booster that can deal with the above letter code. 

The benefit is that we can get information like: 

This base can be either A or G, but not C or U. 

However if you would like to get a taste of using a booster to highlight the bases that are potentially trouble mutating, there already is an early version of a color booster that has marked bases. 

  • White ring = soft constraints - highlight of bases that potential trouble may cause trouble if mutated
  • Red = when one of the soft constraint bases is mutated. 
  • Black bases - bases mutated compared to the original sequence

Here is a link to the script:

Soft constraints for Ribosome Challenge (under development)

To use the booster, Start from copy, under Script type, save as Booster and then Submit script. Then pull the booster under the lightning button when in lab puzzles. It is currently working in the first of the lab puzzles. 

For more detailed help on using a booster, see AndrewKae's guide: 

Quick Start Guide to Using Scripted Tools in Eterna







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Eli Fisker

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  • Color Boosting

Posted 2 months ago

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jandersonlee

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A first cut at the IUPAC constraints is here: https://eternagame.org/web/script/9306696/

It only applies to 5C and the colors still need to be refined. Successful mods are black; if a mod does not satisfy the IUPAC constraints it is pink. Otherwise the color indicates the constraints.

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jandersonlee

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I've also tweaked this booster to work on the 5C+larger constraints puzzle and actually managed to design a sequence that works in all 4 energy models + the IUPAC and larger set of constraints and a few others that work in Vienna+Vienna2+IUPAC. I agree with @whbob: I welcome the extra constraints!