I am using BLAST 2.2.25+ command line version with default penalties.
I have a set of nucleotide sequences. I manually did a 6 frame translation with BioPython and blastp the 6 frames to NR protein.
Using the same set of nucleotide sequences, I also did a tblastx to another set of nucleotide sequences that is not in NR.
Would the bitscores from these two blasts be comparable?
Does tblastx essentially do a 6 frame translation on both nucleotide datasets and blastp them together?