User:Dennis9600

The links below take you to analysis by my lab tool on the currently active labs as of 2013-Sep-08.  In this edition I have added a field for the melt point of each design submitted and I have started to report the result of my forecasting tool.

The forecasting tool looks at factors that have correlated well with past synthesis score.  The current version of the forecasting tool looks at the following factors:

1) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)

2) Whether or not the design folded correctly in the Vienna 2.1.1 Energy Model

3) The melt point of the design (as reported by the EteRNA server)

4) The percentages of C,U, and G in the design, and how far they differ from 13, 10, and 21% respectively (the Berex Strategy).

I have also looked at a) temperature and b) designer's EteRNA points.  Temperature setting of the Energy Model correlated best with past synthesis scores when it was set to the default of 37C.  Designer's EteRNA points had a very weak positive correlation with past synthesis scores so is not used in the forecasting tool.

The current set of labs includes many that have locked bases forming non-canonical pairs.  Past labs have rarely featured designs like that, so my forecasting tool probably shouldn't be very good at forecasting the outcome of these labs.

New reports posted September 13 3:43PM MST:

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2RmVGVDJnUk5RZjA/">Chicken Leg Reversed</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2bXZjSWdsUGZvUE0/">Double 1-3 Loop</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2R1djXzVCNk9vVFU/">ShapeTest 1st State</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2NVRrdG5MRW9PZWs/">ShapeTest 2nd State</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2WThqbGJXUXdyV2c/">G-U_GAGA_Tetraloop_Boost</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2WUJNckw0dDQyRUk/">Hexaloop...</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2UDZMNUhNWEJTVTA/">Large GU Stack</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2d3A4UlY0Nk1qMUE/">Neck Strength Analysis 3 of 3</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2RHBYdFFxd3N4OTA/">Repetitious Sequences</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2LVIzVk9PYi05OTg/">Reversed motor Step 1</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2N21LYy0ycVBndXM/">Robot Serial Killer 3</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2Ty1sczVYM2NzUzg/">Shape Profile - A-C Mismatch</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2TGZGaXV6M3ZtT2M/">SHAPE Profile - A-G Mismatch</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2VWdfblMtSHNDRjg/">SHAPE Profile - C-A Mismatch</a>

<a title="SHAPE Profile - C-C Mismatch" href="https://docs.google.com/file/d/0B-rDnoMjFSH2NTQ2Nnl0dnY3bEE/">SHAPE Profile - C-C Mismatch</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2aDdIMGZnTzVHdTg/">SHAPE Profile - C-U Mismatch</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2dmxyOHl2c0czVmc/">SHAPE Profile - G-A Mismatch</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2S1pkOUdUM2hubEU/">SHAPE Profile - U-C Mismatch</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2TU96WE9JRWlIbzQ/">SHAPE Profile - U-U Mismatch</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2WWhHX2ZuNDN5UDQ/">Unmodified tRNA Sequences</a>

<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2cFA5alo3b0haeE0/">Wobble Quad Stability 1</a>