I have 15 protein sequences of 99 amino acids each. After doing some looking around I have found that there are several ways you can read sequences into R and do pairwise or multiple alignments. I, however, do not know how to probe changes at specific positions. For instance, I would like to know the best way to align a standard sequence with one(1) or several mutant sequences and probe each amino acid position that does not match the standard sequence. In other words seq1 = "standard amino acid seq" and seq2 = "mutant seq", align these 2 and then have a way to ask R to report whether there is a change at position 10, or 11, or 12 and so on such that R reports(for example) TRUE or FALSE for this question. Where all the sequences that have a reported TRUE for a change at position X can be grouped against those that do not have a change at this position.
I'm not even sure that R is the best way to do this, but it's the only language I'm somewhat familiar with.
I hope this makes sense. Any help will be appreciated.