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GENOMIC BASED ANALYSIS - Coggle Diagram

- - - - combination of DNA digestion with 1/more restriction enzyme(s)
      - separation of fragments onto a gell through electrophoresis
      - detection of specific fragments by a DNA probe
    - - very useful & quick method in investigating microbial changes in an environment
        
        Enzymatic digestion of the PCR products
        
        Generation of the gel profile
        
        Amplification of the gene target by fluorescent labelled primers
      - Not abble to detect microorganism in sample
      - Only give an idea of the levels differences in microbial diversity environment
      - Result in different size and height that representative the profile of microbial community in a sample
    - - more selctive polymorphism
        
        Undergo pre-selective and selective PCR amplifications to reduce the fragment numbers
        
        The remaining fragments are run onto gel electrophoresis
        
        The fragments are ligated to adapter
        
        Software is used to interprete the fragment profile
        
        Digestion of DNA
    - - DNA is amplified with universal primer
        
        Amplification of DNA with a universal primer
      - No specific knowledge about the microbial genome is gathered due tousage of universal primer
        
        The gel profile of the individuals will be different as a result of mutation in the primer annealing sites
    - - to differentiate a specific genomic variation
        
        PCR products are denaturised- single strand DNA
        
        PAGE or CGE is used to confirm the presence of any mutation in the genome sequence
        
        Amplication of the genome
- - - - locate the precise position of the complementary segment in cell
      - a fluorescent-labelled segment of RNA/DNA can be used
        
        to detect the presence of a specific complement of the genome in a sample
        
        The microbial sample undergoes fixation
        
        Hybridize through a fluorescent-labelled segment of RNA/DNA and becoming fluorescently labelled oligonucleotides (probes)
        
        The hybridized cells are detected under epifluorescence microscopy
    - - diagnose based on DNA hybridization
        
        Hybridize the labelled target to the slide
        
        Scan the slide in fluorescent scanner
        
        RNA amplification
        
        Analyse using computer
        
        Extract total RNA
- - - - the sequence is compared to universal database of gene sequences; NCBI
    - - Sanger- 1st generation sequencer
      - Ilumina, Pyrosequencing, and Ion Torrent- 2nd generation sequencer
      - Nanopore and Pacific Biosciences- 3rd generationsequencer