Sequence Alignment With An Improved Smith-Waterman Algorithm

• Main Authors: Ying-Chuan Chen, 陳盈全
• Other Authors: Daw-Tung Lin
• Format: Others
• Language: en_US
• Published: 2003
• Online Access: http://ndltd.ncl.edu.tw/handle/33484850008503010257

碩士 === 中華大學 === 資訊工程學系碩士班 === 91 === Deoxyribonucleic acid (DNA) is a genetic material of life. It represents a variety of function for living and gene information. When people analyse the genetic information composed of nucleotide ( G, A, T, and C ), sequence alignment becomes a most important work. It also plays an important role in the field of Computational Biology. Smith-Waterman algorithm is one of the most sensitive algorithms. It has backtrack ability to get the comparison results. In the original Smith-Waterman (SW) algorithm, the final alignment result is only one, which lacks of selectiveness and comparison. After Waterman improved this algorithm, it can get more answers, but it requires high complexity of computation. We proposed an Upper Triangle (UT) algorithm to enhance the results of comparison. Firstly, the upper-triangle array will be determined, and then the local peaks will be detected by scanning the diagonal. Secondly, the local peaks will be regarded as new origins and compute next new matrix. Finally, some subsequences of higher scores is obtained. In other words, the new algorithm can get more different characteristics between two sequences. It is useful to help the future analysis and research. This algorithm requires about half memory than hat of Smith-Waterman algorithm, and reduces the computation time.