User:Omei/Reversed motor - Step 4: Difference between revisions
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<p | <p>I'm going to use this lab as a test of my theory that the barcode interference can be indirect. That is, f the barcode aligns anti-parallel with the neck, it will throw the trailer back over the hairpin.</p> | ||
<p>I started with garydfisher's design that looks very good in the dot plot and has several mods already. But it looked to me like a case where we might well see tail interference. So I ran it through RNA Composer, and the antiparallel alignment did occur. So I than ran the Minimize Structure routine with the default parameters, to improve the estimate of the local interactions. (This takes an hour or so of CPU-bound computation.) Here's a screen shot of what it produced:</p> | <p>I started with garydfisher's design that looks very good in the dot plot and has several mods already. But it looked to me like a case where we might well see tail interference. So I ran it through RNA Composer, and the antiparallel alignment did occur. So I than ran the Minimize Structure routine with the default parameters, to improve the estimate of the local interactions. (This takes an hour or so of CPU-bound computation.) Here's a screen shot of what it produced:</p> | ||
<p>[[File:R3M4_3_(after_minimization).PNG|800px]]</p> | <p>[[File:R3M4_3_(after_minimization).PNG|800px]]</p> | ||
<p>Key to ribbon coloring:</p> | <p>Key to ribbon coloring:</p> | ||
<p style="padding-left: 30px;"><br />Magenta: trailer<br />Yellow: hairpin <br />White: neck<br />Orange: open loop around neck<br />Gray: All the other bases</p> | <p style="padding-left: 30px;"><br />Magenta: trailer<br />Yellow: hairpin <br />White: neck<br />Orange: open loop around neck<br />Gray: All the other bases</p> | ||
<p style="padding-left: 30px;">The atom-level representation in <span style="color: #ff0000;">red</span> marks predicted base triples.</p> | <p style="padding-left: 30px;">The atom-level representation in <span style="color: #ff0000;">red</span> marks predicted base triples.</p> | ||
<p>I then modified the two open loop bases adjacent to the neck and ran the mod through RNA Composer. This time, I didn't bother to do the | <p>I then modified the two open loop bases adjacent to the neck and ran the mod through RNA Composer. This time, I didn't bother to do the minimization, because it predicted I had successfully moved the trailer away from the neck.</p> | ||
<p>[[File:R3M4_3_mod.PNG|800px]]</p> | <p>[[File:R3M4_3_mod.PNG|800px]]</p> |
Revision as of 04:50, 20 October 2013
I'm going to use this lab as a test of my theory that the barcode interference can be indirect. That is, f the barcode aligns anti-parallel with the neck, it will throw the trailer back over the hairpin.
I started with garydfisher's design that looks very good in the dot plot and has several mods already. But it looked to me like a case where we might well see tail interference. So I ran it through RNA Composer, and the antiparallel alignment did occur. So I than ran the Minimize Structure routine with the default parameters, to improve the estimate of the local interactions. (This takes an hour or so of CPU-bound computation.) Here's a screen shot of what it produced:
Key to ribbon coloring:
Magenta: trailer
Yellow: hairpin
White: neck
Orange: open loop around neck
Gray: All the other bases
The atom-level representation in red marks predicted base triples.
I then modified the two open loop bases adjacent to the neck and ran the mod through RNA Composer. This time, I didn't bother to do the minimization, because it predicted I had successfully moved the trailer away from the neck.