I assembled two different genomes and wanted to see how similar they are on both nucleotide and protein levels so I aligned their nucleotide and translated nucleotide sequences. Here are the results I obtained:
Nucleotide identity=90% Protein identity=57%
How would one make sense of this high nucleotide yet low protein identity result? I have been doing a lot of reading and it seems that if the species are close its better to use the DNA sequence to compare, and I believe these two species should be fairly close. However, I am still confused as to why the values would differ so much.
Thanks for your input!