面向微生物代謝網(wǎng)絡(luò)的分析設(shè)計(jì)方法研究.pdf

1、中國(guó)科學(xué)技術(shù)大學(xué)碩士學(xué)位論文面向微生物代謝網(wǎng)絡(luò)的分析設(shè)計(jì)方法研究姓名：夏德國(guó)申請(qǐng)學(xué)位級(jí)別：碩士專業(yè)：計(jì)算機(jī)應(yīng)用技術(shù)指導(dǎo)教師：鄭浩然2011-04-22ABSTRACT ABSTRACT ABSTRACT With the advent of post-genomic era and increasing use of compu-tational techniques, great development have taken pla

2、ce in compu-tational assistant which has numerous applications in systems biology and synthetic biology. There are two fields of the current microbiology research: one is the research on the microorganisms that can be cu

3、ltured in the laboratory and the other is the research on the metagenome which are access directly from the nature enviorement and cannot be cultured in the laboratory. Synthetic Biology, a rapidly growing multidisciplin

4、ary field in the first field, has two complementary goals- further elucidating biological systems through mimicry and producing bioorthogonal systems with new functions. The techniques to archive these goals: search the

5、expected metabolite routes which are exist in the natural world, predict and find new metabolite routes and design the metabolite routes manually based on the prior knowlege. One of the main uses of metagenomics is to qu

6、antify the species present in a metagenome as well as document their functional contribution to the community, however the BCP algorithm doesn't provide any of this information. In metagenomic analysis, an important

7、component is the metabolic networks, for metabolism is a vital cellular process in the complex-ity of the underlying cellular networks in organisms. For the purpose of providing useful assistants to the biologists, we de

8、veloped corresponding method and assistant system based on the metabolic networks according to the respective aquirements of the two fields metioned above. The works include: (1) The intergration of multiple metabolic da

9、tabases. we have designed the process of the intergration, and developed a modified metabolite name matching alogrithm which can improve the accuracy of the matching. (2)The implementation of the metabolic route search a

10、nd design system. we design and implement the metabolic route search function between two metabolites based on one or multiple organisms' networks. A compound transforming map is designed to represent the metabolic n

11、etwork, and also an weight function is developed to weight the edge in the graph. A metabolic route design function is developed to exploring a route from an appointed metabolite. (3) The design of method to predict the

12、bacterial community of metagenome. We model the prediction of bacterial community to an set cover problem, and the design a modified greedy algorithm based on the biological features of the problem to solove this problem