Gene finding:  Prokaryotes vs. Eukaryotes

• Eukaryotes

  • Complex gene structures (exon/introns)
    • D. melanogaster has an average of 4 introns/gene
    • Very long genes (D. melanogaster X gene 160 kb)
    • Very long introns
    • Many introns
    • “Nested”, overlapping, and alternatively spliced genes
    • 5’ UTRs with non-coding exons
    • Long 3’ UTRs
    • Complex transcription machinery
  • ORF-finding alone is not adequate

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