Multiple Alignment Analysis:Improving Memory Requirement of Recursive Dynamic Programming

• Main Authors: Chen-Fong Chou, 周辰峰
• Other Authors: Meng-Fong Chen
• Format: Others
• Language: zh-TW
• Published: 2007
• Online Access: http://ndltd.ncl.edu.tw/handle/58118319098191666492

碩士 === 義守大學 === 資訊管理學系碩士班 === 95 === Bioinformatics is the study of biology and computer technology. The advancement on sequencing technology has made a lot of protein and DNA sequence information available. Sequence alignment has become one of the key techniques in sequence analysis. Dynamic programming is one of the major methods used in pairwise sequence alignment. When extended to multiple sequence alignment, this method requires complexity in time and memory of O(2k nk) and O(nk), respectively, where k is the number of sequences and n the length of a sequence. This raises problems of needing too much resource and cannot be used efficiently. Our study uses recursive dynamic programming to receive multiple sequences as input and do the analysis. In addition, we work on the improvement on memory allocation to ease the resource loading, as well as bring up the notion of “fixed range” to analyze sequence similarity with or without space being added.