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Team:Shenzhen BGIC 0101/Software
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Revision as of 01:48, 26 October 2013
Genovo
Genovo is a Computer-Aided Design（CAD） tool to create genome denovo.
1. operation interface
We developed its GUI & multiple functions basing upon JBrowse, a genome browse with a fully dynamic AJAX interface, which is included in GMOD in the CLOUD toolset.
2. functional plugins
The current version is 1.3. It consists of 14 main plugins belonging to 3 design modules:
NeoChr, NecleoMod, SegmMan
They are used to construct new chromosome structure denovo, modify CDS based on synoymous mutation, split chromosome into fragments with assembly adaptors in different sizes.
The first module, NeoChr, would assist users to grab related genes in different pathways of various organism manually, to rewire genes’ relationship logically*, and to replace genes with orthologs 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 encrypted watermarks*, telomere, loxp sites to build a brand new genome.
The second one , NucleoMod, 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.
The third one, SegmMan will cut chromosome into pieces in different sizes with Gibson, Goldengate, telomere adaptors to them so that they are able to be assembled into whole experimentally. Besides, it adds flanking vector homologous resion and enzyme sites for the preservation and excision from vectors.
SegmMan, in another level, provide a complementary OLSDesign will guide users to get the chrosome fragments by chip and how to assembly them together.
3. software goals
Genovo enables users to create chromosome-like biodevice denovo, from pathway guided selection of gene to the rewire of genes’ relation, from reasonable substitution of genes to alteration of genes’ location along chromosome addition, from modification to CDS sequence to automatically segmentation design globally for assembly.
We hope Genovo would assist users to have their own designed chromosome even if in silico, and hope it would assist researchers in SC2.0 project and futher genome research in pathway level.
