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• Genome annotation


  Identifying the locations of genes, their structures, and their functions in a genome
• Genome annotation process


  1. Sequences decoded

  2. Identify gene locations

  3. Identify coding and non-coding regions

  4. Identify start and stop points of genes

  5. Identify functions of genes
• Databases used for genome annotation

  • GenBank
  • EMBL
  • WormBase
  • FlyBase
• Types of genome annotation

  • Structural annotation: Identification of genomic elements, 3D/4D protein structures, regulatory regions, coding regions, ORFs
  • Functional annotation: Adding biological information, gene expression, protein function
• Structural annotation


  • Differentiate coding and non-coding regions
  • Identify start and stop codons
• Structural annotation methods


  • Experimental data like expressed sequence tags (ESTs)
  • Bioinformatic analyses (ab initio)
• Ab initio annotation


  Annotation methods that start with just the sequence to be annotated
• Open reading frame (ORF)


  A portion of a genome that contains a sequence of bases that could potentially encode a protein, located between start and stop codons
• Reading frames


  DNA is translated per codon (nucleotide triplet)
• Useful ORFs


  • Based on homology approach, BLAST and sequence alignments, degeneracy of codons
• Predicting gene functions


  Using gene knockout approaches like RNAi and CRISPR
• Prokaryotic genes


  • Small genomes have high gene density, no introns, operons (one transcript, many genes), open reading frames (ORFs)
• The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) is designed to annotate bacterial and archaeal genomes