User:Dennis9600: Difference between revisions

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<p><span style="font-size: small;">The links below take you to analysis by my lab tool on the currently active labs.</span></p>
<p><span style="font-size: small;">The links below take you to analysis by my lab tool on the currently active labs.</span></p>
<p><span style="font-size: small;">&nbsp;</span></p>
<p>&nbsp;</p>
<p><span style="font-size: small;">In this lab cycle, there is one special lab ("Impossible Folding II - The Intramolecular G-quadruplex")&nbsp;that has quad-g complexes in the target complex. &nbsp;For that lab only, I have made a special edition of my analysis tools and used the latest Vienna Energy Model 2.1.3 with the -g option which includes a special algorithm that looks for the possibility of quad-g's. &nbsp;A text report and a spreadsheet for this special lab can be viewed by following these links: &nbsp;<a href="https://docs.google.com/file/d/0B-rDnoMjFSH2SC1rakk4T2VlRGc/edit?usp=sharing">Report</a>&nbsp;<a href="https://docs.google.com/spreadsheet/ccc?key=0AurDnoMjFSH2dHA4OEEwM1UwOV9qLW05OUhGeGhGM2c&amp;usp=sharing">Spreadsheet</a>&nbsp;</span></p>
<p><span style="font-size: large;"><strong>Current set of reports and spreadsheets October 21 is in&nbsp;<a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2XzlSMUVHT1BHQ2s&amp;usp=sharing">ReportsActive2013Oct21</a></strong></span></p>
<p><span style="font-size: small;">Please note, the target structure for this special lab is "<span>.........+++...+++...+++...+++....(((((((....)))))))....................."</span></span></p>
<p>&nbsp;</p>
<p><span style="font-size: small;"><span>where "." denotes an unpaired nucleutide, "(" and ")" denote conventionally paired nucleutides, and the "+" indicates Guanines that are participating in a quad-G Complex.</span></span></p>
<p><span style="font-size: small;">In this edition there is a field for the Vienna 2.1.1 melt point of each design submitted.&nbsp; This new field made it into the text reports, but not the spreadsheets.&nbsp; (Something to do for the next publication. &nbsp;Or the next one after that <img title="Smile" src="/wiki/extensions/TinyMCE_MW/jscripts/tiny_mce/plugins/emotions/img/smiley-smile.gif" border="0" alt="Smile" />)<br /></span></p>
<p><span style="font-size: small;"><span><br /></span></span></p>
<p><span style="font-size: small;">In this edition I have added a field for the Vienna 2.1.1 melt point of each design submitted.&nbsp; This new field made it into the text reports, but not the spreadsheets.&nbsp; (Something to do for the next publication.)<br /></span></p>
<p><span style="font-size: small;">My lab tool includes a forecasting tool that looks at factors that have correlated well with past synthesis scores.&nbsp; The current version of the forecasting tool looks at the following factors:</span></p>
<p><span style="font-size: small;">My lab tool includes a forecasting tool that looks at factors that have correlated well with past synthesis scores.&nbsp; The current version of the forecasting tool looks at the following factors:</span></p>
<p><span style="font-size: small;">1) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)</span></p>
<p><span style="font-size: small;">1) Whether or not the design folded correctly in EteRNA's energy model (Vienna 1.8.5)</span></p>
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<p><span style="font-size: small;">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).</span></p>
<p><span style="font-size: small;">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).</span></p>
<p><span style="font-size: small;">I have also looked at a) temperature and b) designer's EteRNA points.&nbsp; Temperature setting of the Energy Model correlated best with past synthesis scores when it was set to the default of 37C.&nbsp; Designer's EteRNA points had a very weak positive correlation with past synthesis scores so is not used in the forecasting tool.</span></p>
<p><span style="font-size: small;">I have also looked at a) temperature and b) designer's EteRNA points.&nbsp; Temperature setting of the Energy Model correlated best with past synthesis scores when it was set to the default of 37C.&nbsp; Designer's EteRNA points had a very weak positive correlation with past synthesis scores so is not used in the forecasting tool.</span></p>
<p><span style="font-size: small;">The current set of labs includes many that have locked bases forming non-canonical pairs.&nbsp; 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.</span></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p><span style="font-size: large;"><strong>New set of reports and spreadsheets posted October 18 is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2dXZDSVZaeVgyQzg&amp;usp=sharing">ReportsActive2013Oct18</a>.</strong></span></p>
<p><span style="font-size: small;">Previous set of reports and spreadsheets posted October 18 is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2dXZDSVZaeVgyQzg&amp;usp=sharing">ReportsActive2013Oct18</a>.</span></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p><span style="font-size: medium;">Previous set of reports and spreadsheets posted October 11 is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2X2NXeC1uWlJqVlk&amp;usp=sharing">ReportsActive2013Oct11</a>.</span></p>
<p><span style="font-size: medium;">Previous set of reports and spreadsheets posted October 11 is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2X2NXeC1uWlJqVlk&amp;usp=sharing">ReportsActive2013Oct11</a>.</span></p>

Revision as of 01:34, 22 October 2013

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

 

Current set of reports and spreadsheets October 21 is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2XzlSMUVHT1BHQ2s&usp=sharing">ReportsActive2013Oct21</a>

 

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 <img title="Smile" src="/wiki/extensions/TinyMCE_MW/jscripts/tiny_mce/plugins/emotions/img/smiley-smile.gif" border="0" alt="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.

 

Previous set of reports and spreadsheets posted October 18 is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2dXZDSVZaeVgyQzg&usp=sharing">ReportsActive2013Oct18</a>.

 

Previous set of reports and spreadsheets posted October 11 is in <a href="https://drive.google.com/folderview?id=0B-rDnoMjFSH2X2NXeC1uWlJqVlk&usp=sharing">ReportsActive2013Oct11</a>.

 

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