Using blastp, the ppos (percentage of positive scoring matches) is:
(number of identical matches)+(number of similar matches)/(alignment length)
But I think that in ppos the importance of identity is low estimated. I looked in BLOSUM62 table and see that the score of identical matches is between 4 to 11 and the score of similar matches is 1 or 2. Then I made this equation:
Similar matches score (smscore) = (number of identical matches)+(1/5 number of similar matches)/(alignment length)
for example if in a 100 AA match, number of identity is 45 and number of similarity is 15 then, ppos is 60% and smscore is 48
I see that it is an score between percentage of identity and percentage of positives. Am I correct? Do I lead my self into a better understanding of similarity of two sequences or mislead my self?
Does blastp itself has any score like my smscore?