Hi, I have a query regarding BLAST specifically blastn and blastx, Why may similarity scores go UP or DOWN after translation ? For example, the percent identity for a sequence in basic blast is 99% whereas in blastx the score is 100%. Why, what causes the change..Why is this please ? I would very much appreciate a detailed explanation please. Thank you
Simple answer: the genetic code.
The same amino acid may be encoded by different codons. So for example, a query sequence may contain CCC, the subject sequence CCA. Not identical at the nucleotide level but when translated to protein, both codons encode proline, so identical as protein sequence.