Genovo Create customized genome de novo ! Whats Genovo Genovo is a - - PowerPoint PPT Presentation

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Genovo Create customized genome de novo ! Whats Genovo Genovo is a - - PowerPoint PPT Presentation

Dec 24, 2022 344 likes •819 views

Genovo Create customized genome de novo ! Whats Genovo Genovo is a Computer-Aided Design (CAD) suite to create genome in silico and guide users to synthesize and assemble it experimentally. Overview GUI Genovo Properties Interfacially,

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Genovo

Create customized genome de novo !

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What’s Genovo

Genovo is a Computer-Aided Design (CAD) suite to create genome in silico and guide users to synthesize and assemble it experimentally.

Overview GUI

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Genovo Properties

Interfacially, Genovo is developed on a genome browser, JBrowse.

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Genovo Properties

Functionally, Genovo is based on GeneDesign, and BioStudio under SC2.0 project, but has great extensions.

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Graphical User Interface

  • Friendly interface

GUI Function Overview

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GUI & Usage

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Function

  • Genovo plugins & usage

Function GUI Application

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1 – NeoChr (Create chromosome)

Modules

2 – NucleoMod (Edit CDSs) 3 – SegmMan (Split sequence)

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Module 1 – NeoChr

  • New Chromosome Designer
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NeoChr

NeoChr would assist users to get genes and

  • ther features to construct a new pathway

then a neo-chromosome.

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NeoChr

The operations include:

  • Grab genes from pathways
  • Rewire genes’ relation *
  • Define genes’ orienation and order
  • Decouple the genes with overlap
  • Add or delete features, telomere, loxp sites to build a

brand new genome.

* this is partially done

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Module 2 – NucleoMod

  • Sequence Modifier
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NucleoMod would allow users to edit several features of genes.

NucleoMod

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NucleoMod

The operations include:

  • Design CRISPR sites for silencing wild type genes only
  • Create & eliminate enzyme sites
  • Optimize & swap codon
  • Smash repeats
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1 of four plug-ins: Design CRISPR sites for silencing wild type genes only

NucleoMod

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4 of four plug-ins: Smash repeats

NucleoMod

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NucleoMod – Compatibility

Mutiple output including GFF, FASTA, SBOL

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Module 3 – SegmMan

  • Segmentation for synthesis
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  • SegmMan would allow users to split

chromosome into fragments in different sizes for assembly.

SegmMan

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  • Analyze the enzyme sites distribution
  • Split neochr into 30k megas, then 10k chunks and 2k minis for

synthesis and experimental assembly

SegmMan

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Design principle

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Design principle

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Design principle

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Complementary – OLSDesigner

  • Segmentation for

chip synthesis

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SegmMan – Complementary

  • 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.

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Application

Application Human practice Function

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Collaboration

  • Cooperation: Shenzhen_BGIC_ATCG

We use NucleoMod to assist other wet team, Shenzhen_BGIC_ATCG, to design the Biobrick

  • ptimized for eukaryons.
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Collaboration

We transform the prokaryon version of cas9 for S.cerevisiae automatically.

  • Firstly, delete five enzymes of biobrick standard, EcoRI, XbaI,

SpeI, PstI, NotI based on synonymous mutation of CDS.

  • Secondly, optimize the sequence for S.cerevisiae according to

codon usage database.

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Collaboration

  • Cooperation: Project SC 2.0

We tried out SegmMan module to automatically split designed yeast_chr07_4_51 into 2k minichunks in command line.

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Human Practice

Human Practice Acknowledgement Application

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Human Practice

Share:

  • Web-based server
  • Software comparison with BioStudio

http://192.185.29.142/~luxujia/jbrowse_no_git/index.html

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Human Practice

Share:

  • Host as 6 team’ regional workshop

Each team shared their ideas and progress, and even established cooprative intention: SUSTC-Shenzhen-A assisted BGIC_ATCG to purchase experimental material.

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Advertisement:

  • T-shirt sale

We tried to sell our designed iGEM shirt to BGI’s employees.

Human Practice

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Acknowledgement

Acknowledgement Application

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Team

  • Shenzhen_BGIC_0101 is a consortium consists
  • f 13 co-culture students from 6 universities.
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Instructors & Advisors

  • Dr. Huanming YANG
  • Dr. Patrick Yizhi CAI
  • Dr. Yu CHEN
  • Mr. Yun WANG
  • Mr. Kang KANG

Miss Yue SHEN

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Sponsors

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Thank you !

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Supplement

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NeoChr

* Node means gene * Arrow means relation Double click = select genes Ctrl + click = change position in window Click = activation <-> repression Shift + click = change gene’s strand

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NeoChr

Add Delete

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2 of four plug-ins: Create & eliminate enzyme sites

NucleoMod

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3 of four plug-ins: Optimize & swap codon

NucleoMod

* www.kazusa.or.jp/codon/‎

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Collaboration

  • Task log
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Collaboration

  • Finally, we recreate the sequence and annotation file.
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Collaboration

Segmentation result – the fasta file of 2k minis