I'm currently working aligning sequences, and I need to compute similarity between pairs of DNA 'words' of a particular length.
For amino acids I am able to use the substitution matrices in Biopython (Bio.SubsMat.MatrixInfo).
However, I haven't found anything similar for DNA, so I read up and found that most systems use a match/mismatch scoring system where each nucleotide match and mismatch is scored and then the scores are summed. This works fine as long as I am only dealing with A, G, C, and T, but I run into problems when I get a sequence containing N or M and the like (meaning nucleotide unknown).
Is there a standard way to handle the situation with unknowns? That is, how do I score A versus N or M versus N?
Thanks in advance.