I translated COI isopod (Tylos granulatus) sequences and found that the correct reading frame was 3. Then I downloaded international sequences (from GenBank) of the same genus and added them to the alignment. However, I found that these have a different reading frame (frame 1).
Basically my original sequences had no stop codons but when I added species of the same genus and tried to translate the alignment, I get stop codons. I need to make sure I have no stop codons before I do any further analyses. Please help!
Also, does this mean a reading frame is specific to species level and not genus?
The reading frame is relative to the start of whatever sequence fragment you are analyzing, that is, an arbitrary choice dependent on your experimental conditions (restriction fragment, sequencing primer) and of no biological consequence whatoever. In vivo, the correct reading frame for the gene is given by the combination of ribosome binding site, TATA box and AUG start codon.
Are you using the correct genetic code when you analyze your sequences? The "invertebrate mitochondrial code" translates UGA as Trp, while the "standard code" (which is what most programs use by default) would see this as a stop codon. So, if your originals sequences didn't have that codon, but some of the additional sequences you downloaded did, and your program is set to "standard code," that might explain your results. Otherwise I would suspect some sequencing error somewhere and look for sequences to exclude.
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