Eastern Europe has the highest lung cancer mortality among men, while northern Europe and the US have the highest mortality among women. In the United States, black men and women have a higher incidence. Lung cancer rates are currently lower in developing countries. With increased smoking in developing countries, the rates are expected to increase in the next few years, notably in China and India. Globally, as of 2010, liver cancer resulted in 754,000 deaths, up from 460,000 in 1990, making it the third leading cause of cancer death after lung and stomach. Of these deaths 340,000 were secondary to hepatitis B, 196,000 were secondary to hepatitis C and 150,000 were secondary to alcohol. HCC, the most common form of liver cancer, shows a striking geographical distribution. In this research work we focus on the molecular similarities between lung (CHRNA5) and liver (NAT2) mutation gene coded protein. In sequence alignment study we use alignment software in order to predict the conserved regions and find out the overall sequence similarity score in lung and liver cancer protein in human. The final results of this project work demonstrate the molecular similarities of the cancer protein. Hence, this work could be useful in the drug docking. This work could be extended in future in structure based drug designing studies and oncology.