Difference between revisions of "Team:Vanderbilt/Software/Stats"

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  <br>
 +
  <div class="dnaStrand" alt="dna strand">
 +
  <img src="https://static.igem.org/mediawiki/2015/a/a6/Vanderbilt_2015_dna_strand_1.png"/>
 +
  <img src="https://static.igem.org/mediawiki/2015/d/d1/Vanderbilt_2015_dna_strand_2.png"/>
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  <img src="https://static.igem.org/mediawiki/2015/2/2a/Vanderbilt_2015_dna_strand_3.png"/>
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<div id="outline-container-orgheadline2" class="outline-2">
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<h2 id="orgheadline2"><span class="section-number-2">1</span> Mutability Score Statistics</h2>
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<div class="outline-text-2" id="text-1">
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<p>
 +
After writing <a href="https://2015.igem.org/Team:Vanderbilt/Software/Development">software to wrap the BioBrick API</a>, we tried to verify the efficacy of our technique by determining how much our algorithm could optimize protein coding sequences available on the Parts Registry. We scanned over 1400 parts on the registry and determined their <a href="https://2015.igem.org/Team:Vanderbilt/Project/Background">mutability scores</a>, before and after optimization.
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</p>
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</div>
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<div id="outline-container-orgheadline1" class="outline-3">
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<h3 id="orgheadline1"><span class="section-number-3">1.1</span> Globally Optimized</h3>
 +
<div class="outline-text-3" id="text-1-1">
 +
<p>
 +
The typical optimization scheme optimizes according to a series of weights, explained in the <a href="https://2015.igem.org/Team:Vanderbilt/Software/Development">software section</a>. This scheme attemps to produce the lowest possible chance of mutation in most cases. On average, this scheme reduced counts as follows:
 +
</p>
 +
 +
<div class="org-src-container">
 +
 +
<pre class="src src-javascript">{
 +
  rateLimitingCodons: 24.489597780859917,
 +
  weightedPyrDimerCount: 17.15401567267683,
 +
  miscSites: 37.601941747572816,
 +
  hairpinSites: 20.033980582524272,
 +
  insertionSequences: 0.13661581137309292,
 +
  antiShineDelgarno: 125.69694868238558,
 +
  deaminationSites: 51.245492371705964,
 +
  repeatRuns: 26.17614424410541,
 +
  homologyRepeatCount: 0,
 +
  alkylationSites: 176.72122052704577,
 +
  methylationSites: 13.169209431345354,
 +
  oxidationSites: 149.94660194174756,
 +
  RFC10Sites: 0.13800277392510402
 +
}
 +
</pre>
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</div>
 +
</div>
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</div>
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</div>
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</div>
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<div class="row" style="margin:0; border: 0; width: 100%;">
 +
  <div class="col-lg-2" style="height:100%">
 +
    <h3><font color="#7e1d2e">Team</font></h3>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Team/About"><font color="#9e515e">About</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Team/Members"><font color="#9e515e">Members</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Team/Attributes"><font color="#9e515e">Attributes</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Team/Sponsors"><font color="#9e515e">Sponsors</font></a>
 +
    <br>
 +
  </div>
 +
  <div class="col-lg-2" style="height:100%">
 +
    <h3><font color="#7e1d2e">Project</font></h3>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Project/Background"><font color="#9e515e">Background</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Project/Sequence"><font color="#9e515e">Sequence</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Project/Circuit"><font color="#9e515e">Circuit</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Project/Organism"><font color="#9e515e">Organism</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Project/Nanopore"><font color="#9e515e">Nanopore</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Project/Achievements"><font color="#9e515e">Achievements</font></a>
 +
    <br>
 +
  </div>
 +
  <div class="col-lg-2" style="height:100%">
 +
    <h3><font color="#7e1d2e">Parts</font></h3>
 +
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Parts/Part_Collection"><font color="#9e515e">Part Collection</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Parts/Optimized_RFPs"><font color="#9e515e">Optimized RFPs</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Parts/Visualizing_Evolution"><font color="#9e515e">Visualizing Evolution</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Parts/Repair Enzymes"><font color="#9e515e">Repair Enzymes</font></a>
 +
    <br>
 +
  </div>
 +
  <div class="col-lg-2" style="height:100%">
 +
    <h3><font color="#7e1d2e">Notebook</font></h3>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Notebook/May"><font color="#9e515e">May</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Notebook/June"><font color="#9e515e">June</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Notebook/July"><font color="#9e515e">July</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Notebook/August"><font color="#9e515e">August</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Notebook/September"><font color="#9e515e">September</font></a>
 +
    <br>
 +
  </div>
 +
  <div class="col-lg-2" style="height:100%">
 +
    <h3><font color="#7e1d2e">Practices</font></h3>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Practices/Safety"><font color="#9e515e">Safety</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Practices/Collaborations"><font color="#9e515e">Collaborations</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Practices/Real_World_Applications"><font color="#9e515e">Applications</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Practices/Interlab"><font color="#9e515e">Interlab</font></a>
 +
    <br>
 +
  </div>
 +
  <div class="col-lg-2" style="height:100%">
 +
    <h3><font color="#7e1d2e">Software</font></h3>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Software/Development"><font color="#9e515e">Development</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Software/User_Guide"><font color="#9e515e">User Guide</font></a>
 +
    <br>
 +
    <a href="https://2015.igem.org/Team:Vanderbilt/Software/Stats"><font color="#9e515e">Statistics</font></a>
 +
    <br>
 +
  </div>
 +
</div>
 +
  <br>
 +
<!-- /footer -->
 +
 +
</div>
 +
 +
<div class="col-lg-1 hidden-sm" style="height:100%;" id="dnaStrand2">
 +
  <br>
 +
  <div class="dnaStrand" alt="dna strand">
 +
  <img src="https://static.igem.org/mediawiki/2015/a/a6/Vanderbilt_2015_dna_strand_1.png"/>
 +
  <img src="https://static.igem.org/mediawiki/2015/d/d1/Vanderbilt_2015_dna_strand_2.png"/>
 +
  <img src="https://static.igem.org/mediawiki/2015/2/2a/Vanderbilt_2015_dna_strand_3.png"/>
 +
  <img src="https://static.igem.org/mediawiki/2015/f/f4/Vanderbilt_2015_dna_strand_4.png"/>
 +
  </div>
 +
</div>
 +
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</div>
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</html>

Revision as of 03:06, 19 September 2015

Vanderbilt iGEM 2015

1 Mutability Score Statistics

After writing software to wrap the BioBrick API, we tried to verify the efficacy of our technique by determining how much our algorithm could optimize protein coding sequences available on the Parts Registry. We scanned over 1400 parts on the registry and determined their mutability scores, before and after optimization.

1.1 Globally Optimized

The typical optimization scheme optimizes according to a series of weights, explained in the software section. This scheme attemps to produce the lowest possible chance of mutation in most cases. On average, this scheme reduced counts as follows: 

{
  rateLimitingCodons: 24.489597780859917,
  weightedPyrDimerCount: 17.15401567267683,
  miscSites: 37.601941747572816,
  hairpinSites: 20.033980582524272,
  insertionSequences: 0.13661581137309292,
  antiShineDelgarno: 125.69694868238558,
  deaminationSites: 51.245492371705964,
  repeatRuns: 26.17614424410541,
  homologyRepeatCount: 0,
  alkylationSites: 176.72122052704577,
  methylationSites: 13.169209431345354,
  oxidationSites: 149.94660194174756,
  RFC10Sites: 0.13800277392510402
}

Team

About
Members
Attributes
Sponsors

Project

Background
Sequence
Circuit
Organism
Nanopore
Achievements

Parts

Part Collection
Optimized RFPs
Visualizing Evolution
Repair Enzymes

Notebook

May
June
July
August
September

Practices

Safety
Collaborations
Applications
Interlab

Software

Development
User Guide
Statistics