Medical DNA databases provide a rich source of genetic and medical data. Researchers probably use this data to find treatments for different disorders, with a of furthering medical research to help people suffering from various conditions and disorders. Medical and pharmaceutical researches use these DNA database for discovering new medicines. Protein sequence alignment is important, as it helps in determining evolutionary relationship, which are descended from a common ancestor. Various techniques are developed and proposed. A binary string is always computation friendly. In this paper we propose a method of determining protein sequence alignment using binary strings, developed using properties of proteins.