I am doing horizontal gene transfer (HGT). My pipeline is based on blast bit-score. So far, I have used blastx (query is a set of my assembled transcripts). Now, I am thinking to use blastp (query is the set of all the translated-ORF from my assembled transcripts).
I am not sure if blastx and blastp will give different bit-scores. I understand that blastx first find the translated-ORF from all frames then run blastp: Am I wrong?
Thanks very much!!