StefanPatman
commented
1 year ago Hello @cebos,
A reading frame of +1 means that the first nucleotide in the sequence will belong to the first codon.
A reading frame of +2 means that the second nucleotide in the sequence will belong to the first codon. So the third nucleotide will belong to the second codon, and the fourth nucleotide will belong to the third codon. As a result, the first nucleotide will also belong to the third codon, like the fourth.
Similarly, a reading frame of +3 means that the third nucleotide will belong to the first codon, thus the first nucleotide will belong to the second codon and the third nucleotide will belong to the third codon.
In essence, "reading frame" states which nucleotide will belong to the first codon.
Also note that the program will "adjust reading frames" by default. This means that sequences will be padded with "?" in the output so that they always start with the first codon. This option also reverse-complements negative reading frames. You can enable/disable this behaviour at the "export" step.
I hope this helps! I remember discussing this option during development and thinking that maybe it wasn't clear enough. If you have any suggestions about how to clarify this concisely, I'd be happy to have a look!
Hi, I would like to use concatenator but am confused but the options for selecting a reading frame, I've provided a screenshot of the options below. If +1 indicates that the open reading frame starts from the first base pair in my alignment, I don't understand why +2 says it corresponds to the 3rd codon position.
Thank you for your time!