I have a bunch of pairwise sequence alignments (simple clustal alignments).
One of the sequences is the reference sequence. I would like to extract the position of the SNPs.
I wrote some code in python, allowing me to extract the position of the SNP in the alignment. Given that position I extracted the 10nt upstream of the SNP and used those 10nt to search the reference sequence. Doing that I was able to get the position of the SNP in the reference. This approach seemed to work well, however I was wondering whether anyone had a solution that would be more elegant?
I would be happy to share my code if people are interested