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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 黃乾綱 | |
dc.contributor.author | Bo-Jun Huang | en |
dc.contributor.author | 黃柏潤 | zh_TW |
dc.date.accessioned | 2021-05-20T20:32:15Z | - |
dc.date.available | 2010-08-06 | |
dc.date.available | 2021-05-20T20:32:15Z | - |
dc.date.copyright | 2008-08-06 | |
dc.date.issued | 2008 | |
dc.date.submitted | 2008-07-30 | |
dc.identifier.citation | 1. Ashburner, M., et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 2000. 25(1): p. 25-9.
2. Boguski, M.S. and G.D. Schuler, ESTablishing a human transcript map. Nat Genet, 1995. 10(4): p. 369-71. 3. Fickett, J.W., Fast optimal alignment. Nucleic Acids Res, 1984. 12(1 Pt 1): p. 175-9. 4. Altschul, S.F. and D.J. Lipman, Protein database searches for multiple alignments. Proc Natl Acad Sci U S A, 1990. 87(14): p. 5509-13. 5. Sprague, J., et al., The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res, 2008. 36(Database issue): p. D768-72. 6. Crosby, M.A., et al., FlyBase: genomes by the dozen. Nucleic Acids Res, 2007. 35(Database issue): p. D486-91. 7. Hubbard, T.J., et al., Ensembl 2007. Nucleic Acids Res, 2007. 35(Database issue): p. D610-7. 8. Chen, Y.C., et al., ZooDDD: a cross-species database for digital differential display analysis. Bioinformatics, 2006. 22(17): p. 2180-2. 9. Wilkinson, M.D. and M. Links, BioMOBY: an open source biological web services proposal. Brief Bioinform, 2002. 3(4): p. 331-41. 10. Oinn, T., et al., Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics, 2004. 20(17): p. 3045-54. 11. Inmon, W.H. and R.D. Hackathorn, Using the data warehouse. 1994, New York: J. Wiley & Sons. xii, 285. 12. Rumbaugh, J., I. Jacobson, and G. Booch, The unified modeling language reference manual. Addison-Wesley object technology series. 1999, Reading, Mass.: Addison-Wesley. xvii, 550 p. 13. Reichhardt, T., It's sink or swim as a tidal wave of data approaches. Nature, 1999. 399(6736): p. 517-20. 14. Achard, F., G. Vaysseix, and E. Barillot, XML, bioinformatics and data integration. Bioinformatics, 2001. 17(2): p. 115-25. 15. Huang, Y., et al., JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration. Bioinformatics, 2003. 19(18): p. 2351-8. 16. Salgado, D., et al., COMPARE, a multi-organism system for cross-species data comparison and transfer of information. Bioinformatics, 2008. 24(3): p. 447-9. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/9627 | - |
dc.description.abstract | 生物學家會利用較常研究的模式動物(model animal) ,透過蛋白質或基因序列的來預測與非模式動物的同源關係。然而,從過去研究的文獻了解,跨物種組織的整合平台與高通量的序列比對系統顯得相當重要。若是缺乏一個整合平台,則研究人員需要先至網站下載欲研究的物種資料,並建構各資料間的關聯性。若尚需考慮跨物種組織的序列比對,操作流程會更加複雜。此外,針對基因功能註解的部分還可以透過GO Term說明。
本論文目的為建構一個跨物種組織分析的系統平台,提供研究人員選擇欲研究的物種與組織進行高通量序列比對,進而協助研究人員對跨物種組織之間的同源性有所了解,而這也是目前大部分的生物資訊系統所缺乏的功能。此外,我們也將序列比對結果與GO功能註解資訊建立連結。最後,我們運用Web2.0的技術提供友好的人機互動介面,並將查詢結果封裝為XML (Extensible Markup Language)格式,以利於未來的信息交流。 | zh_TW |
dc.description.abstract | The biologists expect to use model animal to predict non-model animal when they want to deal with sequence alignment. However, the integrated platform on cross-species and multiple-tissue for gene-protein-function inference is critical according to literature surveys on related service. Without integrated platform, researches have to download files, link the relationships between databases, and develop programs to deal with dataset manually. With the consideration of different species and multiple tissues, the complexity of platform is incredible to deal with multiple data sources for biologists. In addition, function inference for gene sequences could be done by GO (Gene Ontology) term.
In this paper, we propose a framework of integrated platform with cross-species and multiple-tissue data reference, and it provides high-throughput sequence analytic tool for homology mapping. In addition, we also develop a web service to integrate different data sources and functional annotation information of GO. Computer science technology is also applied such as XML (Extensible Markup Language) for information exchange to simplify flow combination and dynamic web design and web 2.0 technology for friendly interactive interface to provide enriched information. | en |
dc.description.provenance | Made available in DSpace on 2021-05-20T20:32:15Z (GMT). No. of bitstreams: 1 ntu-97-R95525052-1.pdf: 906797 bytes, checksum: c978c1bed1fe96b425ac169cd389fd55 (MD5) Previous issue date: 2008 | en |
dc.description.tableofcontents | 口試委員會審定書............................................i
誌謝.......................................................ii 中文摘要..................................................iii 英文摘要...................................................iv 圖次......................................................vii 表次.......................................................ix Chapter 1 緒論..............................................1 1.1 研究動機..............................................1 1.2 研究目的..............................................2 1.3 研究流程..............................................3 1.4 論文架構..............................................4 Chapter 2 文獻探討..........................................5 2.1 相關研究網站..........................................5 2.1.1 NCBI..............................................5 2.1.2 The Gene Ontology.................................5 2.2 資料來源介紹..........................................7 2.2.1 UniGene資料集.....................................7 2.2.2 NR 資料集.........................................8 2.2.3 RefSeq資料集......................................8 2.2.4 GOA (Gene Ontology Annotation, GOA@EBI)...........9 2.2.5 Gene Ontology資料集...............................9 2.3 序列比對工具.........................................10 2.3.1 BLAST簡介........................................10 2.3.2 FASTA格式........................................12 2.3.3 HTML4BLAST工具...................................12 2.3.4 Graphviz 結構關係圖產生器........................13 2.3.5 BlastSummary.....................................13 2.4 相關系統研究.........................................14 2.4.1 COMPARE..........................................14 2.4.2 ZooDDD...........................................14 2.4.3 BioMOBY..........................................15 2.4.4 Taverna..........................................15 Chapter 3 資料倉儲建置.....................................16 3.1 Framework............................................16 3.2 資料倉儲內之物種與組織...............................16 3.2.1 物種.............................................17 3.2.2 組織與發展時期...................................18 3.3 正規化資料來源之表格設計.............................18 3.3.1 正規化UniGene之欄位設計..........................18 3.3.2 正規化NR之欄位設計...............................19 3.3.3 正規化RefSeq之欄位設計...........................19 3.3.4 正規化GOA之欄位設計..............................20 3.3.5 正規化Gene Ontology之欄位設計....................20 3.3.6 整合各資料集之ERD................................22 Chapter 4 系統設計與建構...................................23 4.1 系統運作流程.........................................23 4.2 系統模組介紹.........................................29 4.2.1 模組一 : 物種及組織選擇..........................29 4.2.2 模組二 : FASTA格式之產生與進行BLAST演算..........30 4.2.3 模組三 : Gene Ontology相關資訊之擷取.............34 4.2.4 模組四 :蛋白質序列資訊之擷取與封裝為XML文件形式..35 4.2.5 模組五 : GO樹狀圖形及階層路徑分析與呈現..........37 Chapter 5 討論.............................................41 5.1 與COMPAER系統進行比較................................41 5.2 與ZooDDD系統進行比較.................................43 Chapter 6 結論與未來工作...................................47 6.1 結論.................................................47 參考文獻...................................................49 附錄A : UniGene物種版本及各組織與發展時期的序列數目........51 | |
dc.language.iso | zh-TW | |
dc.title | 支援跨物種組織的整合性高通量序列分析及功能註解參考系統 | zh_TW |
dc.title | Integrated reference system for high-throughput sequence analytic and functional annotation on cross-species and multiple-tissue | en |
dc.type | Thesis | |
dc.date.schoolyear | 96-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 洪振發,丁詩同,林恩仲,蔡孟勳 | |
dc.subject.keyword | 跨物種組織,序列比對工具,基因註解,蛋白質,模式動物, | zh_TW |
dc.subject.keyword | DNA,cross-species,multiple-tissue,BLAST,model animal, | en |
dc.relation.page | 64 | |
dc.rights.note | 同意授權(全球公開) | |
dc.date.accepted | 2008-07-31 | |
dc.contributor.author-college | 工學院 | zh_TW |
dc.contributor.author-dept | 工程科學及海洋工程學研究所 | zh_TW |
顯示於系所單位: | 工程科學及海洋工程學系 |
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