Hi all, I am dealing with multiple sequence alignments (nucleotide sequence, hundreds of them) at the moment. Essentially, I have two situations:
1) The sequences in the alignment are divergent while there is conservation at a particular heptameric stretch of nucleotides that I am interested in- In such case, I can simply make a weblogo and show that this heptameric site is conserved while the rest of the region in the sequence alignment is not. 2) The other situation is when the sequence divergence is little and sequences are almost identical. In such case, even though the heptameric site is conserved, it does not really prove anything since everything else is conserved too.
I am looking for a numerical parameter that can help me to quantify the sequence divergence in a multiple sequence alignment. This way, I can rank my alignments and those with little sequence divergence can simply be discarded. I can focus on the rest then.