I have DNA sequences from my sample. I want to construct their phylogenetic tree. However, I found more than one stop codon in the middle of the sequences after I translated them to amino acid based on 1st codon position, 2nd codon position, and 3rd codon position. I think it is not a good condition because normally we will find the stop codon at the last position of our sequence. So, what shall I do to solve this problem? Please give me your suggestions. Thank you in advance.
First of all, I am not sure that this is a protein coding sequence.
Is this a sequenced mRNA based Reverse Transcribed cDNA sequence or a genomic DNA based PCR fragment. Because if it is a CDS the stop codon must be at the end and only one stop, if it is a cDNA only one stop which is followed by an untranslated region. If it is a genomic DNA you can find so many stop codons because it can happen that it is not a protein coding sequence (maybe it is an intron or an intergeneric region).
It sounds like you are translating all three reading frames of your sequence. There are a further three on the complementary strand. Only one of these will translate to give the protein sequence, the others will not. The incorrect reading frames generate stop codons with surprising frequency.
Dear Sandor,
I want to make sure that the DNA sequence came from genomic DNA. Then, I amplified a part of them (just short length around 300-400 base-pairs) as my DNA target.
After I translated them to amino acid and checked deeply inside the sequence, I found more than one stop codons. So, what shall I do?.. If they are introns, it means that I can delete them directly, right?
Dear Mathew,
Thank you for your opinion. I will consider it.
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