Systems Bioinformatics Computing: DNA Sequence Assembly Optimization

• Main Authors: Fan, Hsiu-Ming, 范修銘
• Other Authors: Chen, Tsung-Teng
• Format: Others
• Language: en_US
• Published: 2009
• Online Access: http://ndltd.ncl.edu.tw/handle/75792681870416864705

碩士 === 國立臺北大學 === 資訊管理研究所 === 97 === DNA sequence assembly is a set of genomic sequences that can be assembled,condensed, and oriented by applying the sequence homology along with mapping information to create a consensus sequence of a chromosome. While larger any genome grows in size, while more difficult it is reassembled in optimization operations. Hence, the DNA sequence assembly problem has been recognized as NP-hard. In this thesis, we first construct a system bioinformatics model. Based upon this model, a DNA optimization algorithm is proposed and developed by not only applying and modifying the shotgun method but also utilizing a especially designed DNA assembly method to solve worldly well-know DNA sequence assembly problem. This newly developed algorithm is called DNA sequence assembly optimization. It first cuts any given DNA sequence into small fragments and then reassembles these fragments into a new sequence. The newly reassembled sequence can match gene engineering requirements for future bioinformatics developments. This DNA algorithm fully utilizes parallelism to conquer computation complexity bottleneck and can solve the DNA sequence assembly problem more efficient. Experimental results for DNA sequence assembly problem solving have shown in O(n^6) polynomial bound.