博碩士論文 91522078 詳細資訊




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姓名 李英準(Ying-Chun Lee)  查詢紙本館藏   畢業系所 資訊工程學系
論文名稱 使用隱藏馬可夫模型偵測人類基因體序列上之長終端重覆序列結構
(Detection of LTR Structures in Human Genomic Sequences Using Profile Hidden Markov Models)
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摘要(中) 在人類基因體序列中,至少有45%的區域屬於跳躍子(Transposable Elements),造成如此大量的原因,與它們在基因體內移動的行為有關,而它們可能隱含了遺傳演化,及基因體增加適應性及變異性的原因。長終端重覆序列反轉錄跳躍子(long terminal repeat retrotransposons)是一個很重要的一類跳躍子,它們有完整的結構及功能,長終端重覆序列中包含有功能的調控區域,我們相信這些重要的區域會在演化過程中保留下來,因此我們在已知的長重覆終端序列上搜尋這些重要的區域,以隱藏馬可夫模型(Hidden Markov Model)代表這些區域,使用這些模型作為辨認基礎,我們可以辨認大部份已知的長重覆終端序列,並正確地分辨各族群,不但能處理結構完整的情況,也能偵測出新的長重覆終端序列,供遺傳演化上之研究。
摘要(英) More then 45% of human genome was annotated as transposable elements (TEs). The expansion of the human genome is resulted from the mobilization of these TEs and they may increase the plasticity and variation in our genome. Long terminal repeat (LTR) retrotransposons are major components in TEs. There are regulatory sites in LTR and we believe that they could be conserved in evolution. Therefore, we search for these significant motifs in the sequence of LTRs and these motifs are used to train Hidden Markov Model (HMM). Using these models as fingerprints, we can detect most of the known LTRs detected by RepeatMasker and LTR instances are classified into families using the predictive models proposed. It could be helpful for evolution analysis.
關鍵字(中) ★ 隱藏馬可夫模型
★ 跳躍子
★ 長終端重覆序列
★ 生物資訊
關鍵字(英) ★ bioinformatics
★ long terminal repeats
★ transposable elements
★ Hidden Markov Models
論文目次 Chapter 1 Introduction 1
1.1 Background 1
1.2 Motivation 3
1.3 Goal 4
Chapter 2 Related Works 5
Chapter 3 Material and Methods 7
3.1 Overview 7
3.2 Implementation 8
3.3 Materials 9
3.4 Generating Profile HMM of LTR motifs 9
3.5 LTR Detection 9
3.6 Model Evaluation 11
Chapter 4 Results 14
4.1 Motif Profiles 14
4.2 Detection Datasets 15
4.3 Comparison between LTR_STRUC and RepeatMasker 15
4.4 Comparison with RepeatMasker 17
4.5 Case Study: HERV15 Recombination 19
Chapter 5 Discussions and Conclusions 21
References 24
Appendix 26
參考文獻 Bailey, T.L. and C. Elkan. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
Bosch, E. and M.A. Jobling. 2003. Duplications of the AZFa region of the human Y chromosome are mediated by homologous recombination between HERVs and are compatible with male fertility. Hum Mol Genet 12: 341-347.
Bowen, N.J. and I.K. Jordan. 2002. Transposable elements and the evolution of eukaryotic complexity. Curr Issues Mol Biol 4: 65-76.
Brown, T.A. 1999. The Repetitive DNA Content of Genomes. In Genomes (ed. F. Kingston), pp. 138. John Weley, New York.
Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
Frech, K., J. Danescu-Mayer, and T. Werner. 1997. A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter. J Mol Biol 270: 674-687.
Hubbard, T., D. Barker, et al. 2002. The Ensembl genome database project. Nucleic Acids Res 30: 38-41.
Hughes, J.D., P.W. Estep, S. Tavazoie, and G.M. Church. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296: 1205-1214.
Juretic, N., T.E. Bureau, and R.M. Bruskiewich. 2004. Transposable element annotation of the rice genome. Bioinformatics 20: 155-160.
Jurka, J. 1998. Repeats in genomic DNA: mining and meaning. Curr Opin Struct Biol 8: 333-337.
Jurka, J. 2000. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 16: 418-420.
Kazazian, H.H., Jr. 1998. Mobile elements and disease. Curr Opin Genet Dev 8: 343-350.
Krogh, A., M. Brown, I.S. Mian, K. Sjolander, and D. Haussler. 1994. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 235: 1501-1531.
Li, W.H., Z. Gu, H. Wang, and A. Nekrutenko. 2001. Evolutionary analyses of the human genome. Nature 409: 847-849.
McCarthy, E.M. and J.F. McDonald. 2003. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362-367.
McCarthy, E.M. and J.F. McDonald. 2004. Long terminal repeat retrotransposons of Mus musculus. Genome Biol 5: R14.
Pierre Capy, C.B., Dominique Higuet, Thierry Langin. 1998a. Classification of Transposable Elements. In Dynamics and Evolution of Transposable Elements, pp. 37. Chapman & Hall, New York.
Pierre Capy, C.B., Dominique Higuet, Thierry Langin. 1998b. Structure of Transposable Elements. In Dynamics and Evolution of Transposable Elements, pp. 15. Chapman & Hall, New York.
Zhang, X. and S.R. Wessler. 2004. Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc Natl Acad Sci U S A 101: 5589-5594.
指導教授 洪炯宗、張猷忠
(Jorng-Tzong Horng、Yu-Chung Chang)
審核日期 2004-7-12
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