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DNA, PROCESS, Annotating a genome, Bacterial genomes, Annotations, FOCUS…

- - - - proteins
      - other components of the cell
    - - genes
        
        considered as the
        
        smallest unit of information
        
        contain
        
        protein coding sequence
        
        in short
        
        CoDing Sequence (CDS)
        
        have same characteristics
        
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        is
        
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        may also contain
        
        other functional regions
        
        that do not encode for
        
        protein sequence
        
        e.g.
        
        certain regions of DNA known as
        
        promoters
        
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        for bacterial genome that are circular, a region denoted as
        
        ori (origin)
        
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        falling in the
- - - - of the
        
        CDS
        
        on the
        
        genome
    - - Manual checking
        
        to ensure that they were
        
        "true" genes
        
        encoding
        
        "true" proteins
- - - - such as
        
        Rapid Annotations using Subsystems Technology (RAST)
        
        using
        
        growing library of subsystems that are manually curated
        
        A subsystem is a set of functional roles that together implement a specific biological process or structural complex. A subsystem may be thought of as generalization of the term pathway.
        
        protein families largely derived from the subsystems (FIGfams)
        
        classifies genes into
        
        functional roles
        
        such as
        
        metabolic pathways
        
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        collection of functional roles
        
        such as
        
        transport systems
        
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- - - - Manual curation
        
        using tools such as
        
        BLASTx
        
        to compare newly identified
        
        CDS
        
        to protein databases such as
        
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    - - using approaches that predicted
        
        Open Reading Frames (ORFs)
- - - - related bacterial pathogens
    - - comparing these
        
        in order to gain more insight into the biology of the
        
        bacterial genome
- - - - for making
        
        polypeptides
        
        are found in a
        
        single untinterrupted sequence
- - - - more reliable
  - - - not complete
    - - gaps
        
        might be missing or truncated from the
        
        genome assembly
- - - - uses
        
        sequence similarity tools
        
        to transfer function from
        
        one known protein
        
        to
        
        an unknown protein
        
        provided they are similar enough