Identitity and similarity- The ratio of identical amino acids residues to the total number of amino acids present in the entire length of the sequence is termed as identity (Figure 39.1). Where as ratio of similar amino acids in a sequence relative to the total number of amino acid present is termed as similarity. The extend of similarity between two amino acids is calculated with a similarity matrix. An alignment between two amino acid sequences is required to calculate identity or similarity score. In the process, two sequence are arbitrarily placed to each other and an alignment score is calculated. This process is repeated until best score is found. In few cases, the length of the amino acids can be enlarged or reduced by incorporating a residue or inserting a gap (Figure 39.1).

Figure 39.1: Sequence alignment of nucleotide and protein sequences.