Team:Shenzhen BGIC 0101/Modules

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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software">Overview</a></div>
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Modules#">Modules</a></div>
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<h2>Modules</h2>
 
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<h2>Neochr</h2>
<h2>Neochr</h2>
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<p>
Neochr module uses public data from <a href="www.yeastgenome.org">Saccharomyces Genome Database</a>, <a href="www.genome.jp/kegg">Kyoto Encyclopedia of Genes and Genomes</a> , <a href="www.genome.wisc.edu">E.coli genome project</a>,<a href="www.mgc.ac.cn/VFs/main.htm"> Virulence Factors of Pathogenic Bacteria </a>.<br/>
Neochr module uses public data from <a href="www.yeastgenome.org">Saccharomyces Genome Database</a>, <a href="www.genome.jp/kegg">Kyoto Encyclopedia of Genes and Genomes</a> , <a href="www.genome.wisc.edu">E.coli genome project</a>,<a href="www.mgc.ac.cn/VFs/main.htm"> Virulence Factors of Pathogenic Bacteria </a>.<br/>
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<img class="hehe" src="https://static.igem.org/mediawiki/2013/8/8c/Delete.png" /><br/>
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<h2>NucleoMod</h2>
<h2>NucleoMod</h2>
<p>When we extract gene from wild type genome to create a new chromosome, We need to silence the original wild type gene. The NucleoMod module can design CRISPR site to reach this goal. And the module can optimize the codon to increase expression level of genes.
<p>When we extract gene from wild type genome to create a new chromosome, We need to silence the original wild type gene. The NucleoMod module can design CRISPR site to reach this goal. And the module can optimize the codon to increase expression level of genes.
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<h2>SegmMan</h2>
<h2>SegmMan</h2>
<p>The synthesizer or synthesis chip can up to 3kb DNA sequence with high accuracy, but chromosome is not that short.<br/>
<p>The synthesizer or synthesis chip can up to 3kb DNA sequence with high accuracy, but chromosome is not that short.<br/>
SegmMan can settle this problem, it splits chromosome into 30k fragments, after parsing its exited enzyme sites, continues segmentation into 10k and 2k fragments. In 10k and 2k level, its will add vector homologous region and design enzyme sites.<br/>
SegmMan can settle this problem, it splits chromosome into 30k fragments, after parsing its exited enzyme sites, continues segmentation into 10k and 2k fragments. In 10k and 2k level, its will add vector homologous region and design enzyme sites.<br/>
<img class="hehe" src="https://static.igem.org/mediawiki/2013/e/ec/Segmentation_principle_general.jpg" /><br/>
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<h2>Others</h2>
<h2>Others</h2>
<p>Presentation from KGML<br/>
<p>Presentation from KGML<br/>
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This module will grab genes’ detail information in KEGG Makeup Language (KGML) file which can be downloaded in KEGG or get through KEGG API, and it will establish a new standard for data transmission which will convert XML format into JSON format and simplify structures. Furthermore, this module will export genes’ list and its relationships. Choose one pathway and this module will visualize the pathway and rebuild it in the level of genes.</p>
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This module will grab genes’ detail information in KEGG Makeup Language (KGML) file which can be downloaded in KEGG or get through KEGG API, and it will establish a new standard for data transmission which will convert XML format into JSON format and simplify structures. Furthermore, this module will export genes’ list and its relationships. Choose one pathway and this module will visualize the pathway and rebuild it in the level of genes.
<img class="hehe" src="https://static.igem.org/mediawiki/igem.org/3/3b/Mod1.png" />
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<h2>Complementary project</h2>
 
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<h3>contact us</h3>
 
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<p>BGI-Shenzhen, Beishan Industrial Zone<br />
 
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Yantian District, Shenzhen, 518083, China</p>
 
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<p> <span>email:</span><br />
 
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<a href="mailto:gongjianhui@genomics.com">gongjianhui@genomics.com</a></p>
 
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<p>BGIC<br/></p>
 
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<h2>Complementary project</h2>
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Revision as of 02:13, 26 October 2013

Neochr

Neochr module uses public data from Saccharomyces Genome Database, Kyoto Encyclopedia of Genes and Genomes , E.coli genome project, Virulence Factors of Pathogenic Bacteria .

The Neochr module contains three plugins: Decouple, Add and delete.





NucleoMod

When we extract gene from wild type genome to create a new chromosome, We need to silence the original wild type gene. The NucleoMod module can design CRISPR site to reach this goal. And the module can optimize the codon to increase expression level of genes.






SegmMan

The synthesizer or synthesis chip can up to 3kb DNA sequence with high accuracy, but chromosome is not that short.
SegmMan can settle this problem, it splits chromosome into 30k fragments, after parsing its exited enzyme sites, continues segmentation into 10k and 2k fragments. In 10k and 2k level, its will add vector homologous region and design enzyme sites.



Others

Presentation from KGML
This module will grab genes’ detail information in KEGG Makeup Language (KGML) file which can be downloaded in KEGG or get through KEGG API, and it will establish a new standard for data transmission which will convert XML format into JSON format and simplify structures. Furthermore, this module will export genes’ list and its relationships. Choose one pathway and this module will visualize the pathway and rebuild it in the level of genes.



Complementary project



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