1
$\begingroup$

I came across this slide:
enter image description here
Now I haven't understood what the last two grey colored lines mean. Can't ORFS be of any size? What is overlapping frames here?

$\endgroup$
3
$\begingroup$

Can't ORFS be of any size?

I think the point being made is that in a random sequence of 64 amino acids, on average 3 out of 64 should be stop codons, because there are three possible nucleotide sequences for stop codons (UAA, UAG, UGA). ORFs could theoretically be any size but the longer the sequence the more likely you are to come across a stop codon purely due to probability.

What is overlapping frames here?

An example of overlapping frames is shown in the slide: enter image description here

For instance, you can see that the first "CU" in the first frame produces an alanine (as GCU), while the "CU" in the second frame produces a leucine (as CUU).

They have the same nucleotide sequence, but are offset to produce different amino acids. Viruses have very "condensed" genomes and often can use the same nucleotide sequence for different genes, just starting at different points in that nucleotide sequence. This means they have functional overlapping frames.

$\endgroup$
  • $\begingroup$ "but the longer the sequence the more likely you are to come across a stop codon purely due to probability." what does this line mean $\endgroup$ – girl101 Nov 5 '15 at 12:20
  • $\begingroup$ so they have considered the frame size to be 3 here $\endgroup$ – girl101 Nov 5 '15 at 12:21
  • 2
    $\begingroup$ @Rishika A reading frame is always 3 nucleotides. All I am saying is that in a random sequence of nucleotides, if you select any three at random you should come across a stop codon 3 out of 64 times. Think of it like driving down a road, where there are traffic lights every few blocks. You might get lucky and have a green light for 5 lights in a row, but it is statistically unlikely that you can avoid a red light for a very long distance. Think of the stop codon like a red light. $\endgroup$ – Harry Vervet Nov 5 '15 at 12:33

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.