Identifying nested/overlapping reading frames in nucleotide sequences I'll start by saying I'm a total stranger to this field, so I'd love to be corrected if I misunderstood something along the way.
I'm writing a python code to identify all the reading frames in a sequence of nucleotides. To my understanding, a reading frame is defined by a start codon and a stop codon, which made total sense to me until I learned you can have nested/overlapping reading frames.
My question is:
Assuming the start codon &quot;AUG&quot;, and the stop codon &quot;UAA&quot;:
AUG AAA GGG AUG CCC UUU UAA AGA CUC UAA
How do you identify the reading frames? Is each stop codon referring to a single start codon? If so, how can you tell to which one?
I tried looking this up and could only come up with articles explaining the effects of overlapping reading frames, rather than how are they interpreted. I would greatly appreciate even a nudge in the right direction.
Please let me know if I was not clear enough or if I got something wrong.
Thanks!
EDIT: After reading the answers here and researching further I learned that ORF identification on DNA sequences isn't as simple as finding a single start and stop codon, and is complicated beyond the scope of my question. I'll probably default to using online tools to do this from now on.
An RNA sequence has six possible reading frames depending on the offset (0, 1, 2) and the direction (forward, reverse complement). All frames can potentially be used for  protein translation, but only one frame per protein (i.e. there is no shifting going on when translation is happening, excluding shifts introduced by splicing).
If you need to find all the possible protein sequences within an RNA sequence, there are plenty of programs already available (e.g. getorf and transseq from the EMBOSS tool kit).