18rRNA gene DNA sequences- coding or non coding for alignment?

Question

[flowerchild4]

I have DNA sequences I acquired from amplification of the 18S rRNA gene of parasite DNA in insects. I am trying to understand the sequencing alignment process as I have all sequences in MEGA with blast matches. For alignment, is this DNA protein coding or not? I was under impression it does not code for protein, only transcribed to RNA. Given options of Align DNA only, or align codons (coding for protein) which is most appropriate? Thanks for helping!

Answer 1

[Michael]

You are right, ribosomal RNA doesn't code for protein, therefore only nucleotide level alignments make sense.