The Application Of Immune Genetic Algorithm To Biological Sequence Alignment

Sequence Alignment is one of the common problems and also one of the most importanttools in bioinformatics research. As the base of bioinformatics research such as geneidentification, molecule evolution and life origin, it compares the similarity of biology data toinfer their functions, structures and evolution informations.Immune Genetic Algorithm (IGA) is a hybrid improved Genetic Algorithm (GA). Itcombines the GA and immune theory by introducing the immune system's characteristics(such as immune regulation mechanism, diversity keeping strategic etc.) into canonical GA. Itcan prevent the premature convergence and other problems in the process of search. So it is abetter optimization search algorithm.In this paper, based on the study of the development of sequence alignment and itsessence, the author designs a coding method for the possible solution of pair-wise sequencealignment and proposes a Pair-wise Sequence Alignment approach based on IGA (PSAIGA).This new algorithm is applied to DNA and protein sequence alignment in the experiment. Theresults demonstrate that the new approach is reasonable and efficient.In this paper, PSAIGA was written in C++. Meanwhile, Needleman-Wunsch (NW)algorithm and Pair-wise Sequence Alignment based on Genetic Algorithm (PSAGA) wererealized too. NW result provided the basis to determine the quality of the PSAIGA results andthe experiment result of PSAGA illustrated that PSAIGA can improve the alignment resultand efficiency apparently. In addition, the user interface to align sequences was written byWindow API.