Hi everyone! I was wondering if there is an efficient way to translate two gene sequences, align them with any of the optimal pairwise aligner algorithms (Needlemann-Wunsh or Smith-Waterman) for protein sequences, and pass the alignment pattern back to the dna sequences. I think you can miss a lot of information if you don't take into account the protein substitution matrices when aligning 2 gene sequences..
Anyway, I was looking for something like this:
that handle Biostrings sequence classes in R.