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11/4/2013: I am struggling with the current round of active labs.  Two issues are just killing my analysis tools:

1) There are non-canonical pairs in the target structures of many of the labs, e.g A-A pairs.  

2) The "tails" that are added to the hook aren't the same any more.  They differ from lab to lab and I haven't figured out how to automate the correct generation of the tails.  Their doesn't appear to be any specification of the tails in the JSON data returned by the html GETs that are available.


If you think you have an answer to any of the above issues, please help me out by sending me a PM.  Thanks in advance for any help!




The links below take you to analysis by my lab tool on the currently active labs.


The most current set of reports and spreadsheets posted October 22 is in ReportsActive2013Oct22


In this edition there is a field for the Vienna 2.1.1 melt point of each design submitted.  This new field made it into the text reports, but not the spreadsheets.  (Something to do for the next publication.  Or the next one after that Smile)

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:

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.


I am (still) thinking about how to add Vienna 2.1.1 melt curves and dot plots to these reports.  I can modify my scripts to generate these, but they are in Postscript format.  I haven't yet figured out how to incorporate them quickly in my reports and spreadsheets.  If you think there is any easy way to do this, please let me know.


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


Happy folding,


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