The frames denote the Open Reading Frames (ORFs) in a nucleotide sequence..For example if you have this nucleotide sequence: AUGCUAGUCUG
So, the first frame starts as: AUG CUA GUC and so on..the second frame starts as: UGC UAG UCU..and the third frame starts as: GCU AGU CUG
Now, the ribozome has 3 windows as mentioned above where it can come and bind and start the translation. We do not know, and hence the software does not know which frame will the ribozome choose to begin translation.
So, all the three results will be fine..This is just a prediction..so, you can go ahead with anyone of the translated sequences..
Both Bhagwan and Prasun have dealt the meaning, so the only thing I should add is about reliability. The six reading frames are "reliable", but one of them has biological meaning, because the Ribosomal machinery has delicate mechanism to select the meaningful reading frame. There is a way of selecting the most likely reading frame, given a NA sequence of reasonable length. There are 61 sense codons (code for an amino acid) and 3 non-sense codons. You have a 3/61 probability of finding an stop codon in a random sequence of bases, grossly 1 of every 20 amino acids. However natural proteins are much longer, so selective pressures ensure a bias towards sense codons. Out of the six possible reading frames, most of the time, only one will give you a reasonably long aa sequence.
Best wishes,
Rogelio
Thank you all for the answers, they were very useful. So, can I choose the best frame which gives me the lower possibility of stop codon in my sequence? Is it acceptable to submit my sequence to a nucleotide sequence database?
There is no difference betwen frame 1 , 2 or 3. It is not always easy to locate first base pair , which code of first amino acid of a protein. This is complex problem due to lack of complete information regarding 5'UTR and TSS .Simplest and brilliant solution was to frame shift by one bp and tranlate given Nucleotide. In this approach ivestigator usually select longest possible open reading frame as most informative peptide sequence.
You don't know how much those informations were useful! Thank you all! Best regards!
Hi, I have another question about the BioEdit software, when I select the "frame 3" the program shows me a message "Acess violation at address 004653E1 in module 'Bioedir.exe'. Write of address 00190AA8". What this means? I got the frame 1 and 2, but I didn't get the frame 3. Why? Thank you so much!
Dear Colleague\
I appreciate to know why when translating nucleotide sequence to amino acid sequence sometimes I found many stars among the aminoacids Agk*fffft*? how this can be resolved, Iam using Bioedit and Mega software?
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