The Bioinformatics (BI) is a sequence alignment, usually three sequences which can be RNA, DNA and proteins. Because the three or more given sequences can be of large lengths, aligning them by hand can be time consuming and in some cases traditionally impossible. Thus BI comes into use thereby aligning each sequence, and revealing the similar part of the given gene. BI finds great use in bioinformatics where it is used to predict the protein structure, its function, family or its domain. These problems are related to AI and can be classified in the NP complete domain of problems. Thus with the goal of identifying maximum similarities among the sequences, we can use various approaches and techniques like Genetic Algorithms (GA) and its variant in BI.