Team:HIT-Harbin/Parts

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                     <div class="site-description"><h4><span class="colored">Team</span></h4></div>
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                     <div class="site-description"><h4><span class="colored">Parts</span></h4></div>
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<p>Sequence optimization was done using JCat(Java Codon Adaptation Tool)[1] developed by  Andreas Grote </p>
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<h5 class="hashed"><span>CODON OPTIMIZATION FOR HRPS AND HRPR GENE</span></h5>
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<img src="https://static.igem.org/mediawiki/2013/f/f8/Hrps_sequence_cai_before_optimization.png"/>
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<p>Figure1: Codon Adaptation of hrpS gene in E.coli before optimization</p>
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<p></p>CAI-Value of the sequence before optimization:0.2736.    GC-Content of the sequence before optimization:59.17%
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<img src="https://static.igem.org/mediawiki/2013/d/d3/Hrps_sequence_cai_after_optimization.png"/>
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<p>Figure2: Codon Adaptation of hrpS gene in E.coli after optimization</p>
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<p></p>CAI-Value of the optimized sequence:0.9832    GC-Content of the optimized sequence:53.60%
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<img src="https://static.igem.org/mediawiki/2013/a/a8/Hrpr_sequence_cai_before_optimization.png"/>
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<p>Figure3: Codon Adaptation of hrpR gene in E.coli before optimization</p>
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<p></p>CAI-Value of the sequence before optimization:0.2490.    GC-Content of the sequence before optimization:57.70
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<img src="https://static.igem.org/mediawiki/2013/8/8b/Hrpr_sequence_cai_after_optimization.png"/>
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<p>Figure4: Codon Adaptation of hrpR gene in E.coli after optimization</p>
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<p></p>CAI-Value of the optimized sequence:0.9721.    GC-Content of the optimized sequence:53.69%
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<h4>reference</h4>
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<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
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An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox.  Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.
 
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Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for  users who wish to know more.
 
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<groupparts>iGEM013 HIT-Harbin</groupparts>
<groupparts>iGEM013 HIT-Harbin</groupparts>

Latest revision as of 02:17, 28 September 2013

HIT-Harbin

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

<groupparts>iGEM013 HIT-Harbin</groupparts>

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