Graphical Representation Of Dna Sequences And Their Similarity Analysis

In recent twenty years, graphical representation techniques of DNA sequences have been found to be very useful in highlighting local and global DNA sequence comparison analysis, and corresponding numerical characterizations and analysis of similarity have been developed that help quantify the visual patterns.In this thesis we start out with a review of 3D DNA graphical representations, and then present recent 2D representations according to degeneracy. Meanwhile, we propose a new 2D graphical method based on a classification of DNA bases, which is suitable to make numerical analysis later. Nevertheless, the focus of this thesis is not only to introduce graphical representations but also to describe several numerical analysis methods based on graphical representations for the comparison of different DNA sequences. In chapter 3 and 4, we use the new graphical representation and Yau[ll]'s representation to make numerical DNA analysis. Moreover, we illustrate these methods by examining dissimilarity of exon-1 of β-globin gene of 11 species, and compare our results with some existing numerical methods. In the last chapter, we briefly discuss analysis of similarity in view of longest common subsequence problem of DNA sequences. The numerical characterizations and analysis of similarity in chapter 3 and 4 are performed by using Matlab 7.0.