Difference between revisions of "User:Dennis9600"

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<p><span style="font-size: medium;">11/4/2013: The results posted so far do not cover all of the active labs for this cycle.&nbsp; :-( </span></p>
 
<p><span style="font-size: medium;">11/4/2013: The results posted so far do not cover all of the active labs for this cycle.&nbsp; :-( </span></p>
 
<p><span style="font-size: medium;">I have been struggling with the current round of active labs.&nbsp; Two issues have been killing my analysis tools: </span></p>
 
<p><span style="font-size: medium;">I have been struggling with the current round of active labs.&nbsp; Two issues have been killing my analysis tools: </span></p>
<p><span style="font-size: medium;">1) There are non-canonical pairs in the target structures of many of the labs, e.g A-A pairs. I am still working on this issue...<br /></span></p>
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<p><span style="font-size: medium;">1) There are non-canonical pairs in the target structures of many of the labs, e.g A-A pairs. </span></p>
 +
<p><span style="font-size: medium;">I have modified my script so that it recognizes the presence of non-canonical pairs, and uses the --nsp option when calling the Vienna RNA tools.&nbsp; However, I don't believe the results that are produced.<br /></span></p>
 
<p><span style="font-size: medium;">2) The "tails" that are added to the hook aren't the same any more.&nbsp; They differ from lab to lab.&nbsp; I have a fix for this issue and you will start to see more and more lab results posted in the folder mentioned above.&nbsp; Thanks to ElNando for info that lead to the fix!<br /></span></p>
 
<p><span style="font-size: medium;">2) The "tails" that are added to the hook aren't the same any more.&nbsp; They differ from lab to lab.&nbsp; I have a fix for this issue and you will start to see more and more lab results posted in the folder mentioned above.&nbsp; Thanks to ElNando for info that lead to the fix!<br /></span></p>
 
<p><span style="font-size: medium;"><br /></span></p>
 
<p><span style="font-size: medium;"><br /></span></p>

Revision as of 15:46, 8 November 2013

Analysis Reports and Spreadsheets produced by my Python script can be found in ReportsActiveLabs.

 

11/4/2013: The results posted so far do not cover all of the active labs for this cycle.  :-(

I have been struggling with the current round of active labs.  Two issues have been killing my analysis tools:

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

I have modified my script so that it recognizes the presence of non-canonical pairs, and uses the --nsp option when calling the Vienna RNA tools.  However, I don't believe the results that are produced.

2) The "tails" that are added to the hook aren't the same any more.  They differ from lab to lab.  I have a fix for this issue and you will start to see more and more lab results posted in the folder mentioned above.  Thanks to ElNando for info that lead to the fix!


If you think you have an answer/suggestion for issue #1 above, please help me out by sending me a PM.  Thanks in advance for any help!

 

In this edition:

 1)  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 a) temperature and b) designer's EteRNA points as possible factors for my forecasting tool.  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.

 

 

Things to do:

I am currently working on a change to my scripts that will do a better job of analyzing labs that have non-canonical pairs locked into the target structure.   The Vienna RNA folding tools have an option to allow non-standard pairs.  This option gives them a pairing free energy of 0, which may not be correct, but may be better than nothing.

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,

---Dennis9600

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