Profiles
Are a variation of the position specific scoring matrix approach just described. Profiles are calculated slightly differently to reflect amino acid substitutions, and the possibility of gaps, but are used in the same way.
In general a profile entry Mla for location l and amino acid a is calculated by
where b ranges over amino acids, wlb is a weight (e.g. the observed frequency of a.a. b in position l) and Sab is the (a,b)-entry of a substitution matrix (e.g. PAM or BLOSUM).
Position specific gap penalties can also be included.