User:Dennis9600

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Revision as of 12:24, 10 November 2013 by Dennis9600 (talk | contribs)

Analysis Reports and Spreadsheets produced by my Python script can be found in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2cDFibWt6T19nRzg&usp=sharing">ReportsActiveLabs</a>.  You can bookmark this folder in your browser.  I have decided to stick with one folder rather than change with each publication cycle. 

 

In this edition:

  1) If the target structure contains locked, non-Canonical pairs, the Vienna tools are called with a --nsp option that allows the pairing and assigns an energy of 0 to it.  Zero may not

be the best value to use, but it seems to be better than not doing anything.

  2) Some of the labs now have a starting sequence of 'GG' instead of 'GGAAA'.  It looks like the devs have left things open for additional "tails" to be used in future labs.  For now, my script

recognizes both of the sequences that have appeared and uses the correct one for each lab.

 3)  There is a field for the Vienna 2.1.1 melt point of each design submitted.  This new field now appears in both the text reports and the spreadsheets.

My lab tool includes a forecasting tool that looks at factors that have correlated well with past synthesis scores.  The current version of the forecasting tool looks at the following factors:

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

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

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

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

    e) log10(designer's EteRNA points).  This factor is given a very low weight.

 

Things I have looked at:

I have also looked at the temperature setting of the energy model as a possible factors for my forecasting tool.  I was suprised to find that the default setting of 37C is the best setting for my forecasting tool.

 

 

Things to do:

1. I am (still) thinking about how to add Vienna 2.1.1 and EteRNA melt curves and dot plots to these reports.  I can modify my scripts to generate these, but they are in Postscript format.  I am investigating Ghostscript and ImagMagick as possible tools to incorporate into my scripts to convert the graphics.  I've been informed that EteRNA dot plots aren't strictly the same as Vienna 1.8.5 dot plots.  I will need to incorporate the modifications that EteRNA made to Vienna 1.8.5 dot plots to get it right.

2. As of 11/10/2013, a new round of synthesis results is available.  I need to run the training portion of my forecasting tool on the new data.

3. Investigate Vienna's "ensemble diversity measure" as another possible factor for the forecasting tool to consider.

4. Look for published energy parameters for non-Canonical pairs in RNA sequences.  There's got to be something better than 0 out there.

5. Look at "upgrading" to Vienna 2.1.3 (from Vienna 2.1.1) in my toolset.

 

Please let me know if you have any other things you would like to see in my lab reports.

 

Happy folding,

---Dennis9600