Team:HIT-Harbin/Judging

From 2014.igem.org

(Difference between revisions)
Line 109: Line 109:
     </div>
     </div>
   </div>
   </div>
 +
  <!--mainarea -->
 +
  <div id="content">
 +
                <div id="subheader-bar">
 +
                    <div class="site-description"><h4><span class="colored"><cufon class="cufon cufon-canvas" alt="Parts" style="width: 54px; height: 20px;"><canvas width="60" height="27" style="width: 60px; height: 27px; top: -7px; left: 1px;"></canvas><cufontext>Parts</cufontext></cufon></span></h4></div>
 +
 +
                </div>
 +
<p>Sequence optimization was done using JCat(Java Codon Adaptation Tool)[1] developed by  Andreas Grote </p>
 +
<h5 class="hashed"><span>CODON OPTIMIZATION FOR HRPS AND HRPR GENE</span></h5>
 +
<div align="center">
 +
<img src="https://static.igem.org/mediawiki/2013/f/f8/Hrps_sequence_cai_before_optimization.png">
 +
<p>Figure1: Codon Adaptation of hrpS gene in E.coli before optimization</p>
 +
</div>
 +
<p></p>CAI-Value of the sequence before optimization:0.2736.    GC-Content of the sequence before optimization:59.17%
 +
<div align="center">
 +
<img src="https://static.igem.org/mediawiki/2013/d/d3/Hrps_sequence_cai_after_optimization.png">
 +
<p>Figure2: Codon Adaptation of hrpS gene in E.coli after optimization</p>
 +
</div>
 +
<p></p>CAI-Value of the optimized sequence:0.9832    GC-Content of the optimized sequence:53.60%
 +
<div align="center">
 +
<img src="https://static.igem.org/mediawiki/2013/a/a8/Hrpr_sequence_cai_before_optimization.png">
 +
<p>Figure3: Codon Adaptation of hrpR gene in E.coli before optimization</p>
 +
</div>
 +
<p></p>CAI-Value of the sequence before optimization:0.2490.    GC-Content of the sequence before optimization:57.70
 +
<div align="center">
 +
<img src="https://static.igem.org/mediawiki/2013/8/8b/Hrpr_sequence_cai_after_optimization.png">
 +
<p>Figure4: Codon Adaptation of hrpR gene in E.coli after optimization</p>
 +
</div>
 +
<p></p>CAI-Value of the optimized sequence:0.9721.    GC-Content of the optimized sequence:53.69%
 +
<h4>reference</h4>
 +
<p></p>[1] Andreas Grote et al.  JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Research 2005 Vol.33
 +
</div>
 +
 +
<!--groupparts-->
 +
 +
<div id="groupparts" style="min-height:100px;width:700px;">
 +
<style>
 +
  .status_cell { width:8px; }
 +
  .status_star { width:2em; }
 +
 
 +
.c4 { width: 80px; white-space:normal; }
 +
.c6 { width: 150px; white-space:normal; }
 +
.c7 { width: 50px; white-space:normal; }
 +
  </style>
 +
<table class=" pgrouptable tablesorter" style="width: 100%;" cellpadding="0" cellspacing="0">
 +
<thead>
 +
<tr><th style="width:8px"></th><th style="width:8px"></th><th style="width:8px"></th><th style="width: 87px;">Name</th><th style="width: 80px" colspan="">Type</th><th style="width: auto;" colspan="">Description</th><th style="width: 150px" colspan="">Designer</th><th style="width: 50px" colspan="">Length</th>
 +
</tr></thead><tbody>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014000">BBa_K1014000</a></td><td>Coding</td><td>HrpS Gene</td><td width="100px">Xiangmiao Zeng</td><td align="right">987</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014001">BBa_K1014001</a></td><td>Coding</td><td>HrpR Gene</td><td width="100px">Xiangmiao Zeng</td><td align="right">948</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014002">BBa_K1014002</a></td><td>Regulatory</td><td>Promoter hrpL</td><td width="100px">Xiangmiao Zeng</td><td align="right">210</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014004">BBa_K1014004</a></td><td>Composite</td><td>HrpR Protein Generator(W)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1168</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014006">BBa_K1014006</a></td><td>Composite</td><td>HrpS Protein Generator(M)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1205</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014007">BBa_K1014007</a></td><td>Composite</td><td>HrpS Protein Generator(W)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1206</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014009">BBa_K1014009</a></td><td>Composite</td><td>tetR Protein Generator(M)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1059</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014010">BBa_K1014010</a></td><td>Composite</td><td>tetR Protein Generator(W)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1060</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014012">BBa_K1014012</a></td><td>Composite</td><td>RFP Protein Generator(M)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1080</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014019">BBa_K1014019</a></td><td>Composite</td><td>HrpR Protein Generator(M)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1168</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_green">A</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014998">BBa_K1014998</a></td><td>Composite</td><td>HrpS Protein Generator</td><td width="100px">Xiangmiao Zeng</td><td align="right">54</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014003">BBa_K1014003</a></td><td>Composite</td><td>HrpR Protein Generator(S)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1169</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_white">&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014005">BBa_K1014005</a></td><td>Composite</td><td>HrpS Protein Generator(S)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1207</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014008">BBa_K1014008</a></td><td>Composite</td><td>tetR Protein Generator(S)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1061</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014011">BBa_K1014011</a></td><td>Composite</td><td>RFP Protein Generator(S)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1082</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014013">BBa_K1014013</a></td><td>Composite</td><td>RFP Protein Generator(W)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1081</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_white">&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014014">BBa_K1014014</a></td><td>Composite</td><td>hrpL AND Gate device</td><td width="100px">Xiangmiao Zeng</td><td align="right">3474</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014015">BBa_K1014015</a></td><td>Composite</td><td>Biological proportional operational Mu-circuit(1)</td><td width="100px">Xiangmiao Zeng</td><td align="right">4540</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014016">BBa_K1014016</a></td><td>Composite</td><td>HrpS Protein Generator</td><td width="100px">Xiangmiao Zeng</td><td align="right">1207</td>
 +
</tr>
 +
<tr>
 +
<td class="status_cell  "></td><td class="status_cell cell_red">U</td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1014997">BBa_K1014997</a></td><td>Composite</td><td>tetR Protein Generator(S)</td><td width="100px">Xiangmiao Zeng</td><td align="right">1324</td>
 +
</tr>
 +
</tbody>
 +
</table></div>
</div>
</div>
<script>toolbar('nav')</script>
<script>toolbar('nav')</script>

Revision as of 12:20, 16 August 2014

Project
  • Abstract
  • Background
  • Design
  • Modeling
  • Results
  • Future Work
Judging
  • Biobrick
  • Achievement
Wetlab
  • Protocols
  • Notebook
Team
  • Members
  • Advisors
  • Instructors
  • Attribution
  • Acknowledge
Human  practic
  • Country Profile
  • Qualification Trials
  • Wechat Platform
  • Video
  • Presentation

Parts

Sequence optimization was done using JCat(Java Codon Adaptation Tool)[1] developed by Andreas Grote

CODON OPTIMIZATION FOR HRPS AND HRPR GENE

Figure1: Codon Adaptation of hrpS gene in E.coli before optimization

CAI-Value of the sequence before optimization:0.2736. GC-Content of the sequence before optimization:59.17%

Figure2: Codon Adaptation of hrpS gene in E.coli after optimization

CAI-Value of the optimized sequence:0.9832 GC-Content of the optimized sequence:53.60%

Figure3: Codon Adaptation of hrpR gene in E.coli before optimization

CAI-Value of the sequence before optimization:0.2490. GC-Content of the sequence before optimization:57.70

Figure4: Codon Adaptation of hrpR gene in E.coli after optimization

CAI-Value of the optimized sequence:0.9721. GC-Content of the optimized sequence:53.69%

reference

[1] Andreas Grote et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Research 2005 Vol.33
NameTypeDescriptionDesignerLength
A  BBa_K1014000CodingHrpS GeneXiangmiao Zeng987
A BBa_K1014001CodingHrpR GeneXiangmiao Zeng948
A BBa_K1014002RegulatoryPromoter hrpLXiangmiao Zeng210
A  BBa_K1014004CompositeHrpR Protein Generator(W)Xiangmiao Zeng1168
A  BBa_K1014006CompositeHrpS Protein Generator(M)Xiangmiao Zeng1205
A  BBa_K1014007CompositeHrpS Protein Generator(W)Xiangmiao Zeng1206
A  BBa_K1014009CompositetetR Protein Generator(M)Xiangmiao Zeng1059
A  BBa_K1014010CompositetetR Protein Generator(W)Xiangmiao Zeng1060
A  BBa_K1014012CompositeRFP Protein Generator(M)Xiangmiao Zeng1080
A  BBa_K1014019CompositeHrpR Protein Generator(M)Xiangmiao Zeng1168
A  BBa_K1014998CompositeHrpS Protein GeneratorXiangmiao Zeng54
   BBa_K1014003CompositeHrpR Protein Generator(S)Xiangmiao Zeng1169
  BBa_K1014005CompositeHrpS Protein Generator(S)Xiangmiao Zeng1207
   BBa_K1014008CompositetetR Protein Generator(S)Xiangmiao Zeng1061
   BBa_K1014011CompositeRFP Protein Generator(S)Xiangmiao Zeng1082
   BBa_K1014013CompositeRFP Protein Generator(W)Xiangmiao Zeng1081
  BBa_K1014014CompositehrpL AND Gate deviceXiangmiao Zeng3474
   BBa_K1014015CompositeBiological proportional operational Mu-circuit(1)Xiangmiao Zeng4540
   BBa_K1014016CompositeHrpS Protein GeneratorXiangmiao Zeng1207
U  BBa_K1014997CompositetetR Protein Generator(S)Xiangmiao Zeng1324

Retrieved from "http://2014.igem.org/Team:HIT-Harbin/Judging"