# User:Meechl

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

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

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 |