Team:Shenzhen BGIC 0101/Modules

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<h1>Neochr - New Chromosome Designer</h1>
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The Neochr module contains three plugins: Decouple, Add and delete.<br/>
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Neochr module uses public data from <a href="http://www.yeastgenome.org">Saccharomyces Genome Database, </a>
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<a href="http://www.genome.jp/kegg">Kyoto Encyclopedia of Genes and Genomes</a> , <a href="http://www.genome.wisc.edu">E.coli genome project</a>,<a href="http://www.mgc.ac.cn/VFs/main.htm"> Virulence Factors of Pathogenic Bacteria </a>.<br/>
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<h1>NucleoMod - Nucleotide Sequence Modifier</h1>
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<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>
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<h1>SegmMan - Split for Assembly</h1>
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<p>The synthesizer or synthesis chip can up to 3kb DNA sequence with high accuracy, but chromosome is not that short.<br/>
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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/>
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<h1>OLS(Oligo library synthesis) Designer</h1>
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<p>For the users who synthesize DNA in chip can utilize OLS(Oligo library synthesis) Designer to design oligos and enzyme sites, primers to assemble 500-800 fragments.</p>
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<p>(a) Pre-designed oligonucleotides (no distinction is made between dsDNA and ssDNA in the figure) are synthesized on a DNA microchip.<br/>
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(b) cleaved to make a pool of oligo nucleotides.<br/>
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(c) Plate-specific primer sequences (yellow or brown) are used to amplify separate plate subpools (only two areshown), which contain DNA to assemble different genes(only three are shown for each plate subpool).<br/>
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(d) Assembly-specific sequences (shades of blue) are used to amplify assembly subpools that contain only the DNA required to make a single gene.<br/>
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(e) The primer sequences are cleaved using either type IIS restriction enzymes (resulting in dsDNA) or by DpnII/USER/λ exonuclease processing (producing ssDNA).<br/>
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(f) Construction primers(shown as white and black sites flanking the full assembly) are then used in an assembly PCR reaction to build a gene from each assembly subpool.<br/>
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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>
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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 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*. Firstly, it would allow users to define gene order and orientation in DRAG&DROP way. Secondly, decoupled these genes if have overlap and make all genes are non-redundancy. Finally, add chromosome features to build a new chromosome and show in the JBrowse. Moreover, users can drag a window in the JBrowse and delete any gene in the window. <br/>
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After constructing a new chromosome, the next step is NucleoMod module which is to modify CDS based on synonymous mutation.
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<h1>Others</h1>
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<h2>NucleoMod</h2>
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<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><br/><br/>
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<h2>SegmMan</h2>
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<h2>Others</h2>
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<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 <a href="http://www.genome.jp/kegg">KEGG</a> 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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<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 15:19, 28 October 2013




Neochr - New Chromosome Designer

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



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


NucleoMod - Nucleotide Sequence Modifier

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 - Split for Assembly

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.






OLS(Oligo library synthesis) Designer

For the users who synthesize DNA in chip can utilize OLS(Oligo library synthesis) Designer to design oligos and enzyme sites, primers to assemble 500-800 fragments.

(a) Pre-designed oligonucleotides (no distinction is made between dsDNA and ssDNA in the figure) are synthesized on a DNA microchip.
(b) cleaved to make a pool of oligo nucleotides.
(c) Plate-specific primer sequences (yellow or brown) are used to amplify separate plate subpools (only two areshown), which contain DNA to assemble different genes(only three are shown for each plate subpool).
(d) Assembly-specific sequences (shades of blue) are used to amplify assembly subpools that contain only the DNA required to make a single gene.
(e) The primer sequences are cleaved using either type IIS restriction enzymes (resulting in dsDNA) or by DpnII/USER/λ exonuclease processing (producing ssDNA).
(f) Construction primers(shown as white and black sites flanking the full assembly) are then used in an assembly PCR reaction to build a gene from each assembly subpool.



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.



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