FAQ and General Questions
Alternative Reading Frames
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 we have 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.