An alignment is a representation of the similarity between 2 nucleotide or protein sequences. In the case of protein sequences, the amino acids derived from ancestral sequences are taken into consideration in the alignment to account for conserved sequence. A pairwise alignment involves 2 sequences and a multiple alignment involves 3 or more sequences. A global alignment involves aligning the entire sequence whereas a local alignment involves aligning subsequences. The optimum alignment is determined by highest score for a given system. In a structural alignment, 3-dimensional structures of proteins under consideration are superimposed (Koonin and Galperin 2003a).