Since the completion of the Human Genome Project (HGP) in 2003, the 3.2 billion basepairs which make up the human genome have been sequenced. These sequences contain the plan for the mechanisms controlling the behavior of each cell. The small variations in the DNA sequence that lead to different characteristics, such as facial features, or color, are known as polymorphisms, which also can cause oral diseases. Periodontitis is a chronic infective disease of the gums caused by bacteria present in dental plaque. Severaazl techniques have been developed to regenerate4 periodontal tissues including guided tissue regeneration (GTR), and the use of enamel matrix derivative (EMD). EMD is an extract of enamel matrix and contains amelogenins. This is evidence to show that amelogenins are involved not only in enamel formation, but also in the formation of the periodontal attachment during tooth formation. Comparative sequence analysis is an approach for detecting functional regions in genomic and protein sequences. Motifs, conserved domains, secondary structure characteristics, and functional sites of proteins related to oral health may be compared, revealing the degree of sequence conservation during vertebrate evolution. Secondary and tertiary structures are important in understanding the function of a protein. In a comparative sequence analysis, the most well-known bioinformatics tools that are used are: basic local-alignment search tool (BLAST), multiple-sequence alignment software (ClustalW), and PROSITE, a database of proten families and domains. The PROSITE database consists of biologically significant sites, patterns, and profiles that help to reliably identify to which known protein family a sequence belongs. Phylogeny Inference Package (PHYLIP) can be used for building phylogenetic trees and a Python-enhanced molecular graphics program (PyMOL) for 3D visualization of proteins.