Research On Pair-wise Sequence Alignment Method In Bioinformatics Based On Genetic-Simulated Annealing Algorithm

Bioinformatics is the science of using computer technology to store, retrieve and analyzebiological information in the field of life sciences. Sequence alignment is a basic informationdisposal method in the study. It is useful for discovering functional, structural, andevolutionary information in DNA and protein sequences. Because sequence data increasesrapidly in biology sequence database, it is very exigent to develop algorithms that have highbiology sensitivity and efficiency. Pair-wise sequence alignment algorithms of Bioinformaicsare studied in this paper.After giving an introduction of all kinds of algorithms in this field and discussing theearliest global pair-wise sequence alignment algorithm ----Needleman-Wunsch DynamicProgramming algorithm, the paper analyzes the disadvantages of all pair-wise sequencealignment algorithms and its heuristic alignment algorithms.Genetic Algorithm is a self-adaptive and self-organizational artificial intelligence whichsimulates nature evolution to obtain best solution as possible. It has a series of operations,such as selection, crossover and mutation. With these operations, it keeps generating new erapopulation and makes population evolved. When evolution stops, populations can cover bestsolution. Because algorithm is easy to be realized and application effect is outstanding,Genetic Algorithm is applied in a lot of domains which contain self-adaptive control,combinatorial combination, pattern recognition, machine learning, and artificial intelligence.Some experimental data show that Genetic Algorithms still has some problems. PrematureConvergence and ebb local searching are still in presence. Simulated Annealing Algorithmsare the complements of the Genetic Algorithms because it has strong local searching.Simulated Annealing Algorithms are random search techniques based on physical annealingprocess, which can prevent the optimizing process into local optimization and get the globaloptimization.On the basis of combining Genetic Algorithm and Simulated Annealing Algorithm forpair-wise sequences alignment, the author has built up corresponding mathematical model.The experiment results indicate that the algorithm is effective and reasonable for pair-wisesequences alignment.