ab initio gene prediction

Question 1

bacteria vs eukaryotes

Answer 1

• much easier for bacteria
• no introns (single coding region)
• smaller intergenic regions
  
  • genes easier to find
  • 2-3% eukaryote genome is genes
• look for largest ORFs
  
  • accurate for low GC
  • high GC → fewer stop codons
    
    • many ORFs will be by chance

Question 2

gene finding programs

Answer 2

• artemis - widely used
• prodigal
  
  • doesn’t just look for ORFs
  • log-likelihood information
  • accuracy >90%
  • performs well with high GC

Question 3

prodigal

Answer 3

• create training set for protein-coding regions
  
  • look for G/C bias at each position of ORFs
  • build model of predicted ORFs with positional bias
• dicodon bias also used
• penalise ORFs downstream of another larger ORF
  
  • difference between 2 scores removed from smaller ORF score
  • add length factor to each
    
    • higher in genome with lwoer GC
• iteration
• dynamic programming

Question 4

log-likelihood

Answer 4

• dicodon bias in exons vs introns
• store statistics and look at random chance of them appearing
• score as log-likelihood of signal to background for each potential gene

Question 5

prodigal iteration

Answer 5

• on sequences with coding score above threshold
• store initiation site with highest score for each ORF
• exmaine starts for ATG/GTG/TTG frequency and RBS/SD
  
  • rescore
• new set of starts with highest score in each ORF selected
• continue iterating and refining

Question 6

prodigal dynamic programming

Answer 6

• performed over all start-stop pairs
• score each gene on start and dicodon scores
• allow some overlap
  
  • opposite strands particularly
  • smaller overlap on same strand
• determine final gene prediction

Question 7

eukaryotic gene prediction

Answer 7

• introns and exons
• variable number and length
• multiple transcripts
  
  • mechanism not fully understood
  • look for enhancers etc.
• large intergenic regions
• need to identify functional sites and patterns around them
  
  • PWM