User:Meechl

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Hi, I'm Meechl. Welcome to my wiki page!


R scripts (wiki page on how to use R scripts)

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While working on labs a few days ago, for some reason I decided that I needed to know the best tetraloop structure. So, I attempted to find out by looking at past lab results. So far, my data includes Cloud labs 0, 69, 71, 72, 73, and 74. In total, I scored 7,032 tetraloops. (I didn't score the barcode.) 4,132 may seem like a lot, but when you consider there are 4096 possible tetraloops... not so much. The vast majority of possible tetraloops were not tested at all. 

I score each tetraloop out of 100 based on the SHAPE score of each base. Closing bases got credit for having reactivities <0.75 and the bases in the loop got credit for having reactivites >0.25. For each type of tetraloop, I found the average score. 

These are the scores of the tetraloops with at least 10 trials: 

<colgroup><col width="61"></col> <col width="46"></col> <col width="40"></col> </colgroup>
Hairpin Score Trials
CGAACG 90.74 18
CGUGAG 90.00 20
GGAGAC 89.91 38
CGUAAG 89.58 24
UGAAAA 89.39 88
GCGUAC 88.89 12
GAAAAC 88.24 493
GCUUGC 88.03 39
CAAAAG 87.88 1650
UGAGAG 87.60 645
GGAAAC 87.20 1115
CGAAAG 86.81 2116
CGAGAG 86.74 44
UGAAAG 85.83 20
AGAAAU 85.75 124
UAAAAA 85.07 67
UAAAAG 84.92 63
CUUCGG 81.22 126
AAAAAU 75.36 23

 

And... They all scored pretty well. (AAAAAU is a possible exception). The results used to look more exiting (varied) before I found an error in my calculations. :(  

I still haven't taken out data with lots of error, or checked to make sure I haven't made any more errors. 

 


 

Scores for all designs in Cloud Lab 70 (unbound vs bound w/ FMN. Mimic Structure = Target FMN Bound Structure):

https://docs.google.com/spreadsheets/d/1fu5fPJjnmibxcuVUOdIKZnlIHACQpAI2w6my9727jwA/edit?usp=sharing

 

Data from Cloud Lab 70:

https://docs.google.com/spreadsheet/ccc?key=0AppiCUq-Rq1tdHl5MUpRSmlscVVzMFJCVGNXb3hjbFE&usp=sharing

 

Graphs comparing the data between switches using FMN and a mimic sequence:

https://docs.google.com/spreadsheets/d/1K2Zp-75Im-34U78f0-zv-HG5kro1RsKDEzm6SLp8S7E/edit?usp=sharing

 

Attempts to score the switches:

https://docs.google.com/spreadsheets/d/1tZ9aRKxw2U30iKrZulkuLlU_jdOP60mSZVrPtqAyGKw/edit?usp=sharing

My Current Switch Score Guidlines (See Brourd's and my talk for discussion):

  • Bound state is defined as the mimic structure
  • All bases with shape data are scored (79 total)
  • Each base can score MaxReward(5), ReducedReward(3), MinReward(1), or zero
  • Sum of scores for each base is divided by highest possible score to get the final score shown in the google doc
  • A base is considered paired if SHAPE reactivity is <0.5 and unpaired if >0.25

Table of how bases were scored. Cases not listed in table scored 0.

Target Shape of Unbound Target Shape of Bound SHAPE reactivity of Unbound Shape reactivity of Bound Score
Paired Paired <0.5 <0.5 MinReward
Unpaired

Unpaired

>0.25 >0.25 MinReward
Paired Unpaired <0.5 >0.25 (and at least 0.25 > unbound) MaxReward
Paired Unpaired any at least 0.25 > unbound ReducedReward
Unpaired Paired >0.25 <0.5 (and at least 0.25 < unbound) MaxReward
Unpaired Paired any at least 0.25 < unbound ReducedReward
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