I'm a bit confused and would appreciate your assistance, please.
I'm trying to use the
pairwiseAlignment function from the
Biostrings package to align two protein sequences.
I'm not quite sure where to put my reference sequence, the sequence I want to compare to. Is it under "subject" or "pattern"?
Also, is the score I get the edit distance? Is it the alignment score? Or is it the the alignment length? When I use local alignment, will the score be higher the more the sequences resemble each other? And when I use global alignment, will the score be lower the more the sequences resemble each other?