Seaweeds are the subset of a larger group known as the algae. It has been widely used in many countries as a source of food and additionally has biomedical and industrial applications such as cosmetic, paint, crop, textile, paper, rubber, and building industries.The marine algae are essential to nature and directly valuable to humans since they have antioxidant, antimicrobial, antiviral, anticancer, anticoagulant and heme agglutinating properties. Moreover, nitrogen containing seaweeds are generally useful as good nutritive source for plants used as fertilizers. Further their applications extend in industrial level as weight reducer, raw materials for fuel production and useful adsorbent for waste water treatment. Moreover, these seaweeds have many beneficial effects and hence could be developed into potential products for biomedical and industrial applications. In this research study we found out the potential mutation gene and to perform protein sequence analysis, protein modeling using Bioinformatics tools. There are three steps involved in our present research investigation. The protein primary structure analysis, Secondary structure analysis and protein three dimensional structure prediction.