Thesis (M.Sc.) - Cairo University - Faculty of Computers and Information - Department of Information System

The DNA{u2019}s linear structure is considered one of the most important points in sequence comparison in biology. The reason of using sequence comparison is to identify the functional, structural and evolutionary relationships between the DNA and proteins sequences. Sequence alignment allows researchers to {uFB01}nd the similar-ities and di{uFB00}erences among genetic sequences, such as DNA and proteins. It can be used in di{uFB00}erent {uFB01}elds like {uFB01}nding homology, exploring the origin of a sequence and identifying protein shape. Many algorithms were developed to perform this task and several hardware existing platforms are suitable for this purpose. Many methods can be used in sequence alignment, including dynamic programming and heuristic methods. The most interesting problem in sequence alignment is sequenc- ing long sequences, many algorithms have been developed to solve this problem using dynamic programming, heuristic methods and statistical methods. In this thesis, we introduce a new DNA-DNA global pairwise sequence alignment tech-nique for improving the accuracy of sequence alignment. The proposed approach uses a new scoring matrix to produce the alignment which is 3empirical codon substitution matrix3. This matrix can be used to discover new relationships be-tween sequences that couldn{u2019}t be discovered using the traditional matrices. Finally we present the experimental results that show the performance of our technique against to 3pairwise align codons3 and 3EMBOSS needle3. We compared the performance time and the alignment score among the three techniques

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