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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 莊曜宇(Eric Y. Chuang) | |
dc.contributor.author | Yi-Fang Lee | en |
dc.contributor.author | 李沂芳 | zh_TW |
dc.date.accessioned | 2021-06-08T02:38:12Z | - |
dc.date.copyright | 2018-07-23 | |
dc.date.issued | 2018 | |
dc.date.submitted | 2018-07-20 | |
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dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/19968 | - |
dc.description.abstract | 現今隨著次世代定序技術之成本顯著下降,建構未知細菌物種的完整基因體或是從環境樣本中提取大量微生物資訊對於研究者而言更為容易,在細菌的定序資料不斷增加累積之下,細菌基因體的相關研究重要性不斷上升,更逐漸成為生物資訊的熱門研究主題。完整基因體的組裝可以有助於了解生物之相關功能和訊息傳輸方式,而如今也有相當多的生物資訊工具和演算法被開發來研究原核生物基因序列,不過如何有效的組合各第三方軟體來創建有效的分析流程是為一大挑戰,尤其複雜的參數設定和以指令列為基礎的軟體操作更成為了研究者分析的阻礙。為了有效解決上列問題,我們以創建對使用者友善的線上分析系統為目標,旨在提供有效而易於操作的細菌全新基因體組裝和宏基因體學資料分析流程,並以Illumina公司平台產出之次世代定序資料作為輸入,在系統中直接提供包括序列品質評估、基因體組裝、基因預測以及基因功能性分析等功能。整體而言,此平台將可大幅節省研究者進行細菌基因體全新組裝或是分析環境樣本的時間與精力,有助於使用者專注深入瞭解目標細菌之致病性或是微生物之生態組成。 | zh_TW |
dc.description.abstract | Nowadays, the substantial reduction of experimental cost in the next-generation sequencing techniques makes it feasible to assemble a de novo bacterial genome of unknown species and acquire plenty of genetic information from environmental samples. With the explosive accumulation of bacterial sequencing data, the research focusing on bacterial genome has become more and more important and popular. The development of the whole genome can help to elucidate biological functions and signaling pathways. Many bioinformatics tools and algorithms have been developed to study prokaryotic genome; however, how to efficiently construct pipelines to integrate all the data poses a major challenge. Complex parameters settings and the command line-based packages cause a great entry barrier for researchers. To address these issues, this study aims to develop an online analytical system with a user-friendly interface to support both de novo assembling and metagenomic analysis pipelines. Multiple analytical steps, including reads cleaning, genome assembly, gene prediction, and functional annotation can be directly performed on the system. In conclusion, this analytical system can greatly reduce the time and efforts for assembling a de novo bacterial genome and analyzing metagenomic samples, which can improve the understanding of the etiology in targeting bacterial species and the ecology of microorganisms. | en |
dc.description.provenance | Made available in DSpace on 2021-06-08T02:38:12Z (GMT). No. of bitstreams: 1 ntu-107-R05945010-1.pdf: 2663313 bytes, checksum: 1ea0db887f3f98c456b3c0c8305ae60e (MD5) Previous issue date: 2018 | en |
dc.description.tableofcontents | Chapter 1. Introduction and Background 1
1.1 Motivation 1 1.2 Specific Aims 2 1.3 Background 4 1.3.1 Bacterial Genome 4 1.3.2 Next-Generation Sequencing 5 1.3.3 De Novo Assembly 7 1.3.4 Metagenomics 8 1.3.5 Bioinformatics Pipeline Framework 9 Chapter 2. Materials and Methods 11 2.1 System Implementation 11 2.2 Reference-Guided and Non-Reference Guided De Novo Assembly 11 2.2.1 Quality Control and De Novo Assembly 12 2.2.2 Gene Prediction Model Comparison and Assessment 14 2.2.3 Functional Analysis, and Phylogenetic Tree 15 2.3 Metagenomic Analysis Pipeline 17 2.3.1 Quality Control, Contamination Removal and Assembly 17 2.3.2 Taxonomic Abundance Counting 17 2.3.3 Gene Prediction, Clustering, and Abundance 18 2.3.4 Functional Annotation, Abundance, and Domain Mapping 18 Chapter 3. Results 21 3.1 Website Interface 21 3.1.1 Parameter Settings and Task Submission 21 3.1.2 Job Queueing and Status Monitoring 22 3.1.3 Result Pages 23 3.2 Resource Usage 24 3.3 Example I: De Novo Assembly of E. coli EC4437 25 3.3.1 Analysis Result 25 3.4 Example II: Metagenomic Analysis of Hot Spring Samples 27 3.4.1 Dataset 27 3.4.2 Analysis Result 28 Chapter 4. Discussion 31 4.1 Performance evaluation 31 4.2 System Feature Comparison 32 4.3 Example I: De Novo Assembly of E. coli EC4437 33 4.4 Example II: Metagenomic Analysis of Hot Spring Samples 35 4.5 Limitation and Future work 37 Chapter 5. Conclusions 40 Figures 42 Tables 54 References 62 | |
dc.language.iso | en | |
dc.title | 建構全面性細菌基因體全新組裝之線上系統 | zh_TW |
dc.title | Development of a Comprehensive Online System for Bacterial De Novo Genome Assembly | en |
dc.type | Thesis | |
dc.date.schoolyear | 106-2 | |
dc.description.degree | 碩士 | |
dc.contributor.coadvisor | 盧子彬(Tzu-Pin Lu) | |
dc.contributor.oralexamcommittee | 蔡孟勳(Mong-Hsun Tsai),賴亮全(Liang-Chuan Lai),倪衍玄(Yen-Hsuan Ni) | |
dc.subject.keyword | 細菌,全新組裝,宏基因體學,使用者友善,線上系統, | zh_TW |
dc.subject.keyword | bacteria,de novo assembly,metagenomics,user-friendly,online system, | en |
dc.relation.page | 67 | |
dc.identifier.doi | 10.6342/NTU201801747 | |
dc.rights.note | 未授權 | |
dc.date.accepted | 2018-07-23 | |
dc.contributor.author-college | 電機資訊學院 | zh_TW |
dc.contributor.author-dept | 生醫電子與資訊學研究所 | zh_TW |
顯示於系所單位: | 生醫電子與資訊學研究所 |
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