Please enable JavaScript.

Coggle requires JavaScript to display documents.

Annotation - Coggle Diagram

- - - - Biological input: codon bias in coding regions, gene structure (start n stop codons, typical exon and intron length, presence of promoters, presence of genes on both strands etc)
      - Covers cases where input sequence contains no gene, partial gene, complete gene, multiple genes
    - - Does not address multiple splicing
      - Could combine two exons from consecutive genes together
- - - - Exons of a few 100 bases may be separated by kilobases of intron
  - - - Extrinsic content sensors
        
        Use homology searches (FASTA + BLAST) to identify highly conserved exons in DB
        
        Largely effective but a significant failing of extrinsic approaches is that they are limited to homologies within DB; if no homologs exist no data can be extracted
      - Intrinsic content sensors
        
        Focus on specific innate characteristics of DNA sequence itself; helps to predict likelihood of whether the sequence 'codes' for a protein or not
        
        Useful intrinsic content sensors include the following
        
        Nucleotide composition
        
        Codon usage
        
        Base occurrence periodicity
  - - - Transcriptional signal sensors (TSS)
        
        Include initiator or cap signal located at transcriptional start site and the upstream TATA box promotor signal
        
        Includes polyadenylation signal (a consensus AATAAA hexamer) located 20 to 30 bp downstream of coding region
      - Translational Signals
        
        Includes 'Kozak signal' (GCC[A/G]CCaugC[not U] located immediately upstream of start codon
      - Splice signals
        
        Since higher Euk genes have multiple exons -> accurate gene structure prediction in these organisms relies on identification of splice site signals
        
        Specifically donor and acceptor sites (GT-AG on introns sequence)
        
        And branch points (CU[A/g]A[C/U]) located 20-50bp upstream of AG acceptor
- - - - Eukaryotic promotor database (EPD) in order to be included in EPD the promotor needs to be
        
        Recognised by eukaryotic RNA POL II
        
        Active in higher eukaryote
        
        Experimentally defined or homologous to an experimentally defined promotor
        
        Biologically functional
        
        Distinct from other promotors in DB
      - JASPAR and TRANSFAC
        
        DBs on eukaryotic cis-acting regulatory DNA elements and trans-acting factors ranging from yeast to human
      - TransTerm
        
        Translation Termination Signal Database: DB of termination and initiation codon contexts