Answers.Body: <p>There are 6 reading frames.  Three forward, three in the reverse direction.</p>
  <p>An Open Reading Frame, an ORF, is a sequence which begins with a start codon, and ends with a stop <strong>in the same frame</strong>.  You find them by looking for sequences that fit that pattern.</p>
  <blockquote>
  <p>Is each stop codon referring to a single start codon? If so, how can
  you tell to which one?</p>
  </blockquote>
  <p>You could have two different transcripts for the same gene with different start codons but the same stop codon.  But in general, the protein translation apparatus will not accidently read through a stop codon.</p>
  <p>And yeah, I hope you are doing this for fun, because obviously people have already made publicly available tools to find ORFs.</p>
  
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Answers.CreationDate: 2020-09-29T06:04:39.283Z
Answers.Text: Yes I am doing this fun, and looking at [orf finders](https://www.ncbi.nlm.nih.gov/orffinder/) results at the same time to compare and figure out how it does what it does. I'm still having some trouble understanding: Given a single frame (out of the six) - I may encounter a frame with 100 start codons and 300 stop codons, and rest coding for amino acids. Can we actually locate the ORF's in a case like this? If so, these are the "rules" I'm looking for. Thanks for the reply!
Answers.UserDisplayName: JayLeeman
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-29T16:54:25.967Z
Answers.Text: If you want to know how ORF finders work, why don't you...look at how ORF finders work?
Answers.UserDisplayName: swbarnes2
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Answers.LastActivityDate: 2020-09-28T23:09:28.887Z
Answers.UserDisplayName: swbarnes2
Answers.Body: <p>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).</p>
  <p>If you need to find all the possible protein sequences within an RNA sequence, there are plenty of programs already available (e.g. <a href="http://emboss.bioinformatics.nl/cgi-bin/emboss/getorf" rel="nofollow noreferrer">getorf</a> and <a href="http://emboss.bioinformatics.nl/cgi-bin/emboss/transeq" rel="nofollow noreferrer">transseq</a> from the EMBOSS tool kit).</p>
  
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Answers.LastEditDate: 2020-09-28T20:25:22.120Z
Answers.UserDisplayName: gringer
Body: <p>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.</p>
  <p>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.</p>
  <p>My question is:</p>
  <p>Assuming the start codon &quot;AUG&quot;, and the stop codon &quot;UAA&quot;:</p>
  <p><strong>AUG</strong> AAA GGG <strong>AUG</strong> CCC UUU <strong>UAA</strong> AGA CUC <strong>UAA</strong></p>
  <p>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?</p>
  <p>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.</p>
  <p>Please let me know if I was not clear enough or if I got something wrong.</p>
  <p>Thanks!</p>
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-28T11:07:37.267Z
Comments.Text: Hi @JayLeeman better to post the code. Simple answer is to translate from each start point and assess length of the exon against the number of stop codons, i.e. maximising the length of the exon. There are 6 possible reading frames, 3 forward, 3 reverse. If you have an idea of the structure of the protein, e.g. surface antigen you can assess GPI anchors and hydrophobic alpha helices as the end of the gene
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-28T23:11:36.350Z
Comments.Text: There is no reason at all for an exon to have either a valid stop or start codon.  If introns are in the sequence the whole enterprise is a waste of time.
Comments.UserDisplayName: swbarnes2
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-29T05:57:27.947Z
Comments.Text: @swbarnes2 This actually clears a lot out of me, thanks! Just clarifying: If I'm reviewing a DNA sequence, it still has introns. If there are introns, how can I locate the ORF's without being able to splice the introns "manually"?
Comments.UserDisplayName: JayLeeman
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-29T17:04:48.200Z
Comments.Text: You cannot programicly know where introns are.  You can only make good guesses.  Or, you have to look up what introns people have empirically determined in your sequence.
Comments.UserDisplayName: swbarnes2
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-29T19:05:54.627Z
Comments.Text: I'll look into that, sounds extremely interesting. Thank you!
Comments.UserDisplayName: JayLeeman
Tags: <rna-seq>
Title: Identifying nested/overlapping reading frames in nucleotide sequences
ThreadText: # Identifying nested/overlapping reading frames in nucleotide sequences
  
  (Asked by: username_0 on 2020-09-28)
  
  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 "AUG", and the stop codon "UAA":
  
  **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.
  
  **Tags:** rna-seq
  
  > **Comments:**
  > **username_1**: Hi @username_0 better to post the code. Simple answer is to translate from each start point and assess length of the exon against the number of stop codons, i.e. maximising the length of the exon. There are 6 possible reading frames, 3 forward, 3 reverse. If you have an idea of the structure of the protein, e.g. surface antigen you can assess GPI anchors and hydrophobic alpha helices as the end of the gene  
  > **username_2**: There is no reason at all for an exon to have either a valid stop or start codon.  If introns are in the sequence the whole enterprise is a waste of time.  
  > **username_0**: @username_2 This actually clears a lot out of me, thanks! Just clarifying: If I'm reviewing a DNA sequence, it still has introns. If there are introns, how can I locate the ORF's without being able to splice the introns "manually"?  
  > **username_2**: You cannot programicly know where introns are.  You can only make good guesses.  Or, you have to look up what introns people have empirically determined in your sequence.  
  > **username_0**: I'll look into that, sounds extremely interesting. Thank you!  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2020-09-28. Score: 1 | Accepted answer
  
  There are 6 reading frames. Three forward, three in the reverse direction.
  
  An Open Reading Frame, an ORF, is a sequence which begins with a start codon, and ends with a stop **in the same frame**. You find them by looking for sequences that fit that pattern.
  
  > Is each stop codon referring to a single start codon? If so, how can
  > you tell to which one?
  
  You could have two different transcripts for the same gene with different start codons but the same stop codon. But in general, the protein translation apparatus will not accidently read through a stop codon.
  
  And yeah, I hope you are doing this for fun, because obviously people have already made publicly available tools to find ORFs.
  
  > **Comments:**
  > **username_0**: Yes I am doing this fun, and looking at [orf finders](https://www.ncbi.nlm.nih.gov/orffinder/) results at the same time to compare and figure out how it does what it does. I'm still having some trouble understanding: Given a single frame (out of the six) - I may encounter a frame with 100 start codons and 300 stop codons, and rest coding for amino acids. Can we actually locate the ORF's in a case like this? If so, these are the "rules" I'm looking for. Thanks for the reply!  
  > **username_2**: If you want to know how ORF finders work, why don't you...look at how ORF finders work?  
  
  ---
  
  ### Answer by username_3 on 2020-09-28. Score: 0
  
  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](http://emboss.bioinformatics.nl/cgi-bin/emboss/getorf) and [transseq](http://emboss.bioinformatics.nl/cgi-bin/emboss/transeq) from the EMBOSS tool kit).
  
  
  ---
  
  