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Team:Shenzhen BGIC 0101/Home
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Revision as of 05:11, 27 September 2013
All members of our team.
Nucleotide modification allow users to modify sequence as their wishes by utilizing codon synonomousness.
We can help you creat a new chromosome.
Genove can help you design a new pathway.
test
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5Genovo
Genovo is a Computer-Aided Design（CAD） tool to create genome denovo. The current version is 1.2. It consists of 10 plugins belonging to 3 design modules.
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 DRAP&DROP way, and add chromosome features to build a brand new genome automatically.
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.
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.
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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SegmMan
SegmMan
SSegmMan will cut chromosome into pieces in different sizes. And it adds fragments with Gibson, Goldengate, Telomere adaptors to them so that they are able to be assembled into whole experimentally.
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NucleoMod
NucMod
NucleoMod can modify CDS based on synoymous mutation. It has 5 applications. Firstly, NucleoMod is used to design CRISPR sites on NeoChr so that we can silence the wild type genes. Secondly, it can erase specific enzyme sites according to the users' selection. Thirdly, users can create a enzyme site in selected region of specific genes. Fourthly, it can optimize the codon efficiency to incresase the expression level. Finally, it can smash the tandem repeat bases to reduce the synthesis difficulty.
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NeoChr
NeoChr
NeoChr is used to construct new chromosome. It would assist users to grab related genes in different pathways manually, to rewire genes’ relationship logically$1, and to replace genes with ortholog that score higher$2. 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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