General Questions

Alternative ORFs
Q: What if there's a possible Shine-Dalgarno sequence and start codon on the opposing strand in the middle of the gene you're working on? Do you assume that the computer has already marked it as a possible gene or do youhave to examine it as well?

A: No, let's stick to our pre-marked genes. There are many ATGs in a genome, and many possible SD sequences. But if the ORF does not code for anything real, it is a red herring.

Alternative ORFs'
Q: What if there's a possible Shine-Dalgarno sequence and start codon on the opposing strand in the middle of the gene you're working on? Do you assume that the computer has already marked it as a possible gene or do youhave to examine it as well?

A: No, let's stick to our pre-marked genes. There are many ATGs in a genome, and many possible SD sequences. But if the ORF does not code for anything real, it is a red herring.

Q: How do we rate our judgment calls? Can we indicate confidence levels?

A:Confidence levels (listed low to high)

• Hypothetical protein: choose if selected "hypothetical protein" under "gene product"
  
• Conserved hypothetical protein: choose if selected "conserved hypothetical protein" under "gene product"
  
  • Not enough info to select "Family Membership" or "Function unclear"
  • no domains identified
  • no family membership)
    
• Family membership: Choose if conserved hypothetical protein identified via PFam or TIGRfam as belonging to a protein family but function and specificity are unclear.
  
• Function unclear: Choose if
  • protein domain is identified
  • protein function is unclear
  • if "putative" or "possible" or "predicted" occur in all the significant Tigrfam, COG, or PFAM names
    
• Specificity unclear: Choose if only more general information on the function of a protein family is available
  • e.g., ABC transporter (but can't predict substrate)
  • e.g., Histidine kinase (but can't predict target response regulator)
• High confidence in function and specificity: Choose if all significant observations agree with each other
  • Clear function
  • Clear specificity