Predicting the Functional Effect of Amino Acid Substitutions and Indels
Examples of computing and interpreting delta alignment scores for six different known variations, (A) deleterious substitution (MIM:151623), (B) neutral substitution (dbSNP:rs1042522), (C) deleterious deletion (MIM:219700), (D) neutral deletion (dbSNP:rs72471101), (E) deleterious insertion (MIM:164200), and (F) neutral insertion (dbSNP:rs10625857) with respect to the selected homologous proteins.
The amino acid residue replaced, deleted, or inserted is indicated by an arrow, and the difference between two alignments is indicated by a rectangle. Low delta scores are interpreted as deleterious, and high delta scores are interpreted as neutral. The BLOSUM62 and gap penalties of 10 for opening and 1 for extension were used.