Team:Shenzhen BGIC 0101/Software

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<h1>Overview：Genome Design Suite</h1>
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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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<p>Genovo is a <b>Computer-Aided Design（CAD） suite</b> to assist users to create new system denovo.</p>
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It sets us free in the laborious, complex creating procedure, including choosing genes of new system (here the system refers to new pathways which is in form of a chromosome), changing chromosome’s structure, editing coding DNA sequence, splitting the chromosome into equipped fragments for synthesis and assembly.
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Genovo’s UI is mainly developed on a genome browser, <a href="http://www.gmod.org/wiki/JBrowse">Jbrowse</a> interface<br/>
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Functionally, Genovo is partially based on <a href="http://54.235.254.95/gd/">GeneDesign</a> algorithm suite, and BioStudio development environment under <a href="http://syntheticyeast.org/">SC2.0 project</a>, but it has great extensions.
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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 to create genome denovo. The current version is 1.2. It consists of 12 plugins belonging to 3 design modules
 
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The first module, NeoChr, 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. Then it would allow users to define gene order and orientation in DRAG&DROP way, and decouple the genes with overlap. In the end, it would add or delete features, such as telomere, loxp sites to build a brand new genome automatically.
 
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The second one , NucleoMod, would optimize the CDS regions and reduce their synthesis difficulty. And it helps design the CRIPSR site so that we can silence the wild type genes, and in the meanwhile, differentiate the wild type and synthesis type when assemling. This module also can erase or create enzyme site locally.
 
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The third one, SegmMan will cut chromosome into pieces with different sizes with Gibson, Goldengate, Homologous adaptors to them so that they are able to be assembled into whole experimentally.
 
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SegmMan, in another level, provide a complementary OLSDesign will guide users to get the chrosome fragments by chip and how to assembly them together.
 
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Genovo would enable users to create chromosome-like biodevice on their bent, and even futher genome research in pathway level.</p>
 
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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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Latest revision as of 16:09, 28 October 2013





Overview：Genome Design Suite

Genovo is a Computer-Aided Design（CAD） suite to assist users to create new system denovo.


It sets us free in the laborious, complex creating procedure, including choosing genes of new system (here the system refers to new pathways which is in form of a chromosome), changing chromosome’s structure, editing coding DNA sequence, splitting the chromosome into equipped fragments for synthesis and assembly.

Genovo’s UI is mainly developed on a genome browser, Jbrowse interface



Functionally, Genovo is partially based on GeneDesign algorithm suite, and BioStudio development environment under SC2.0 project, but it has great extensions.



Retrieved from "http://2013.igem.org/Team:Shenzhen_BGIC_0101/Software"