I want to compare two MSAs of the same set of protein sequences and determine which is better(I do not have the 'true alignment'). One way is the sum of pairs method. But I think sum of pairs is defined for a column in an alignment(average of scores of all pairs of residues). So, how do we calculate the score for the whole alignment? Do we again average the average scores obtained for each column?
If this is the alignment and I am using BLOSUM62 as the scoring matrix.
The SOP for column 1 will be sc(AV)+ sc(VC)+ sc(AC)= a1 (let)
Similarly, for column 2 will be sc(-V)+sc(VV)+sc(-V)=a2
and then for column 3 will be sc(KA)+sc(AK)+sc(KK)=a3
Now, for the score of the MSA, do I take the average of a1 , a2, a3 ?
And then use this score as a metric to compare between two MSAs?
Please let me know of any papers or resources that talk about this. Thanks