The objective of this thesis is to improve the analysis of DNA and protein sequences. Sequence analysis is an important step in drug design to find the relationship among DNA sequences, protein sequences and their functions. The effectiveness of a drug is very much dependent on the correct associations of the sequences to their functions. In this thesis, three novel methods have been developed to enhance the analysis of DNA and protein sequences. Two of the methods target the alignment and prediction of motif sites in DNA sequences. Their improvements are made by introducing joint and vector weight matrix scoring scheme. The third method targets the protein secondary structures, by using new classification indices. The new results show that the structures can be classified into more categories as compared with the existing methods, which hydrophobicity factor is solely considered as a classification index.Master of Engineering (MAE
