Biological Sequences Alignment

With the development of Human Genome Project(HGP), bioinformatics has developed one of the most important subject. Bioinformatics can be defined as a collection of mathematical ,statistical and computational methods for analying biological sequences, that is, DNA ,RNA and amino acid (protein) sequences. Sequence aligment is the most basic and important method. By sequence alignment, we can discover functional, structural and evolutionary information in biological sequences. So, sequence aligment is the basic of bioinformatics.In the chapter 1 of this article, we first introduce the methods of the sequences alignment and scoring schemes. Sequences alignment contain global alignment and local alignment. From the number of the sequence, sequences alignment contain pair-wise sequence alignment and multiple alignment. Then, we give some methods of sequences alignment algorithm. In the chapter 2, We give the BLAST algorithm(Basic Local Alignment Search Tool). BLAST algorithm is based on statistics, and we will prove BLAST algorithm from two different ways. In the chapter 3 , we describe HMM and explain how a HMM can be used to produce a multiple alignment algorithm for numbers of sequences. In the chapter 4, we discuss local graph alignment and motif search in biological networks. Based on this scoring function, we develop a search algorithm for topological motifs called graph alignment, a procedure with some analogies to sequence alignment.In the end, we discuss the problem of the BLAST algorithm,Hidden Markov Models and graph alignment. And then we give some suggestions for the future.