User:Meechl

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

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

<a href="https://github.com/Meechl/MeechlsRScripts">Github</a>

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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:

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.

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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