Comparison Of Biological Sequences And Construction Of Phylogenetic Trees

In molecular biological field,the primary structure of a biological molecule is the detailed description of its atomic composition and the chemical bonds connecting those atoms.Biological sequence alignment is an important and valuable initial pail of bioinformatics.If one wants to know the difference between a sequence and another or a group of sequences,the only way is to compare and analysis the sequences.However,the "phylogeny" describes the relationships between entities(such as species,genes,or genomes)in such a way as to reflect their evolutionary histories.The research fields in this passage focus on comparison of biological sequences and construction of phylogenetic trees.We will propose a novel method by introducing detailedly the traditional methods,then check analysis.The full passage consists of four chapters.The main content is shown as following.Chapter One:Introduction.Firstly this part introduces the history and research status of bioinformatics.Then we come up with the future development direction and application field for bioinforrmatics.As the same time,we have a brief description for comparison of biological sequences and construction of phylogenetic trees.Chapter Two:comparison of biological sequences.In this chapter,firstly the methods of comparison of biological sequences are divided into two classes:alignment algorithms and alignment-free algorithms.The classical alignment algorithms are based on dynamic programming algorithm—the Needleman-Wunsch algorithm and the Smith-Waterman algorithm.However,a lot of researchers have completely broken away from the basic alignment algorithm frame and proposed a large number of effective alignment means(the alignment-free methods).With the development of graph theory,we use the graph tools represent the DNA sequences,and then predict the similarity between sequences by graphical comparisons,for example,2D and 3D.In this part we will focus on LZ complexity algorithm.Chapter Three:construction of phylogenetic trees.This chapter puts forward on the base methods of construction of phylogenetic trees.We will describe distance-based method,character-based method(including Maximum Likelihood,Maximum Parsimony method,Fuzzy cluster and kernel method)and information-based method(Bayesian method).Then,we will introduce the complexity of algorithm,point of view,scope of application and advantage.Chapter Four:the instances of phylogenetic trees construction.This chapter will apply the new methods mentioned above based on the previous three chapters,including weighted similarity measure theory and 0-1 characteristic matrix.We will use the optimization approach to find the best parameter by using MATLAB program.Then we will make sure the feasibility for the methods using experiments.At last,we may proof the highest efficiency and the extensive practicability by using test data.