Team:Shenzhen BGIC 0101/Project

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== Project Details==
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Project#overview">overview</a></div>
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Project#plug-in">plug-in</a></div>
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Project#tutorial">tutorial</a></div>
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<h1></h1>
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<br/>
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<a name="overview"></a>
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<article class="clearfix" style="background: rgba(29, 28, 28, 0.79);">
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<h2>Genovo</h2>
 +
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<div class="post-content" style="color: #ADFFCF;"><hr/><p>Genovo is a Computer-Aided Design (CAD) tool used for denovo design of genome. The current version consists of 4 parts. </p>
 +
<p>The first, Chromosome Construction will grap genes in a common pathway and chromosome features to build a new genome and let user to define the order and orientation in drap-drop way. The second, Nucleotide Modification will optimize and soften the sequence of CDSs. It also help design the CRIPSR sites so that we can silence the wild type genes. The third, Chromosome Segmentation will cut chromosome into pieces and add 3A & Gibson & Goldengate & Homologous Recombination adaptors to the pieces automatically for assembly. The last one, OLS Design will guide users to gain the chromosome by microarray. </p>
 +
<p>Genovo will enable user to design their innovative chromosome as their wishes and further the research on genome on pathway level.</p>
 +
<br/><br/>
 +
<h2>Plug-in</h2>
 +
<hr/>
 +
<a name="plug-in"></a>
 +
<a name="plug1"></a>
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<p>NeoChr</p>
 +
<p>Neochr module would assist users to grab related genes in different pathways manually, to rewire genes’ relationship logically*, and to replace genes with ortholog that score higher*.</p><hr/>
 +
<a name="plug2"></a>
 +
<p>NucleoMod</p>
 +
<p>NucleoMod is a module to modity CDS sequence of genes which generated by Neochr module. This module contains 5 plugins: CRISPR design, erase enzyme site, create enzyme site, codon optimization, repeat smash. All of these plugin is allow user to change or optimize the gene. After NucleoMod operation, the next step is SegmMan to design synthestic method according to the length of chromosome.</p><hr/>
 +
<a name="plug3"></a>
 +
<p>SegmMan</p>
 +
<p>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><hr/>
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<hr/>
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</div>
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</div>
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<a name="tutorial"></a>
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<footer style>
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<div class="seven columns" id="footer-contact">
 +
<h3>contact us</h3>
 +
<p>BGI-Shenzhen, Beishan Industrial Zone<br />
 +
Yantian District, Shenzhen, 518083, China</p>
 +
<p> <span>email:</span><br />
 +
<a href="mailto:gongjianhui@genomics.com">gongjianhui@genomics.com</a></p>
 +
</div>
 +
<div class="four columns" id="footer-project">
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<h3>sponsor</h3>
 +
<p>BGIC<br/></p>
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=== Part 2 ===
 
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=== The Experiments ===
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=== Part 3 ===
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== Results ==
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Latest revision as of 04:12, 28 September 2013

logo


Genovo

Genovo is a Computer-Aided Design (CAD) tool used for denovo design of genome. The current version consists of 4 parts.

The first, Chromosome Construction will grap genes in a common pathway and chromosome features to build a new genome and let user to define the order and orientation in drap-drop way. The second, Nucleotide Modification will optimize and soften the sequence of CDSs. It also help design the CRIPSR sites so that we can silence the wild type genes. The third, Chromosome Segmentation will cut chromosome into pieces and add 3A & Gibson & Goldengate & Homologous Recombination adaptors to the pieces automatically for assembly. The last one, OLS Design will guide users to gain the chromosome by microarray.

Genovo will enable user to design their innovative chromosome as their wishes and further the research on genome on pathway level.



Plug-in

NeoChr

Neochr module would assist users to grab related genes in different pathways manually, to rewire genes’ relationship logically*, and to replace genes with ortholog that score higher*.

NucleoMod

NucleoMod is a module to modity CDS sequence of genes which generated by Neochr module. This module contains 5 plugins: CRISPR design, erase enzyme site, create enzyme site, codon optimization, repeat smash. All of these plugin is allow user to change or optimize the gene. After NucleoMod operation, the next step is SegmMan to design synthestic method according to the length of chromosome.

SegmMan

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.

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