A novel two-tier multiple sequence alignment algorithm

Multiple sequence alignment is one of the basic research areas in bioinformatics. In most cases while doing multiple sequence alignment, a totally unaligned set of sequences are used as an initial data. In this work, we have used Clustal X 2.0.11 program to process those initial data in some aligned way. Then roulette wheel selection operator is used to select the optimal cut points of sequences. Dynamic programming is used to align the subset sequences. By comparing both these two process we found that the result is gradually improving. Our result has proved that we got higher score. In the paper “Shyi-Ming Chen, Chung-Hui Lin, and Shi-Jay Chen; Multiple DNA Sequence Alignment Based on Genetic Algorithms and Divide-and-Conquer Techniques nternational Journal of Applied Science and Engineering; 2005; 3, 2:89-100” we have observed that for the same sequences final score was 25. But using ourmethod we got the final score 32. Some experimental results has shown using graph in order to test the proposed approached.