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Neochr
Neochr module uses public data from Saccharomyces Genome Database, Kyoto Encyclopedia of Genes and Genomes , E.coli genome project, Virulence Factors of Pathogenic Bacteria .
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.
After constructing a new chromosome, the next step is NucleoMod module which is to modify CDS based on synonymous mutation.
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
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.
