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研究生:陳伯良
研究生(外文):Pak-Leong Chan
論文名稱:建立病毒檢測探針設計之平台
論文名稱(外文):A Platform to Aid Probe Design for Virus Identification
指導教授:張猷忠洪泂宗
指導教授(外文):Yu-Chung Chang
學位類別:碩士
校院名稱:國立中央大學
系所名稱:資訊工程研究所
學門:工程學門
學類:電資工程學類
論文種類:學術論文
畢業學年度:92
語文別:中文
論文頁數:38
中文關鍵詞:棎針設計
外文關鍵詞:bioinformatics
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  • 點閱點閱:72
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病毒辨認越來越重要,因為病毒不但傳播得很快,而且傳播範圍很廣。在很多的例子中因為沒有很快的辨認病毒而造成了人命和財產的損失。如果有一個資訊系統能夠結合生物科技很快的辨認病毒則病毒學家就會有充份時間去研究應付病毒的方法。我們設計一個病毒探針資料庫,結合快速的演算法,可以在很短的時間找出最佳的生物晶片探針組合來辨認一組病毒。而且我們把整個系統實現在網際網路讓世界各地的使用者能使用我們的系統,另外我們開發一個程序能驗證最佳探針的辨別能力。
Virus identification becomes more and more important. Virus not only spreads widely, but also infects swiftly. In many cases, virus causes severe crises of health and economic loss. If a system integrating biotechnology to identity virus quickly is developed, virologists will have sufficient time to make a strategy of solution and control it. We develop a system and made use of a fast algorithm to aid virus probe design for microarray. This microarray can identity a group of viruses. The system is implemented and published to the internet so that all users can access the system through the internet at any time. The specificities of optimal probes are verified by the local alignment tool.
Chapter 1 Introduction 1
Chapter 2 Related Works 3
2.1 Microarray 3
2.2 Criteria for designing probes 4
2.3 Optimal probe for microarrays 7
Chapter 3 System and Methods 8
3.1 Data preparation 8
3.2 Generating probe candidates 9
3.3 System flow 10
Chapter 4 Algorithms and Implementation 13
4.1 The longest increasing subsequence algorithm 13
4.2 Selecting the optimal probe 17
4.3 Verifying the selection of optimal probe 18
Chapter 5 Results 21
5.1 The online system 21
5.2 Comparison of different methods in probe design 26
5.3 Evaluation of selection of optimal probe 26
Chapter 6 Discussions 30
References 37
Buechen-Osmond, C. and M. Dallwitz (1996). "Towards a universal virus database - progress in the ICTVdB." Arch Virol 141(2): 392-9.
Chang, P. C. and K. Peck (2003). "Design and assessment of a fast algorithm for identifying specific probes for human and mouse genes." Bioinformatics 19(11): 1311-7.
Delcher, A. L., S. Kasif, et al. (1999). "Alignment of whole genomes." Nucleic Acids Res 27(11): 2369-76.
Gusfield, D. (1997). Algorithms on Strings, Trees and Sequences, Cambridge University Press.
Kaderali, L. and A. Schliep (2002). "Selecting signature oligonucleotides to identify organisms using DNA arrays." Bioinformatics 18(10): 1340-9.
Kane, M. D., T. A. Jatkoe, et al. (2000). "Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays." Nucleic Acids Res 28(22): 4552-7.
Le Novere, N. (2001). "MELTING, computing the melting temperature of nucleic acid duplex." Bioinformatics 17(12): 1226-7.
Li, F. and G. D. Stormo (2001). "Selection of optimal DNA oligos for gene expression arrays." Bioinformatics 17(11): 1067-76.
Mrowka, R., J. Schuchhardt, et al. (2002). "Oligodb--interactive design of oligo DNA for transcription profiling of human genes." Bioinformatics 18(12): 1686-7.
Onodera, K. and U. Melcher (2002). "VirOligo: a database of virus-specific oligonucleotides." Nucleic Acids Res 30(1): 203-4.
Rahmann, s. (2002). "Rapid large-scale oligonucleotide selection for microarrays." In proceeedings of the First IEEE Computer Society Bioinformatics Conference(CSB).
Rahmann, S. (2003). "Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics." IEEE Computer Society Bioinformatics Conference (CSB'03).
Rice, P., I. Longden, et al. (2000). "EMBOSS: the European Molecular Biology Open Software Suite." Trends Genet 16(6): 276-7.
Rouillard, J. M., C. J. Herbert, et al. (2002). "OligoArray: genome-scale oligonucleotide design for microarrays." Bioinformatics 18(3): 486-7.
SantaLucia, J., Jr. (1998). "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics." Proc Natl Acad Sci U S A 95(4): 1460-5.
Wang, X. and B. Seed (2003). "Selection of oligonucleotide probes for protein coding sequences." Bioinformatics 19(7): 796-802.
Zhang, H. (2003). "Alignment of BLAST high-scoring segment pairs based on the longest increasing subsequence algorithm." Bioinformatics 19(11): 1391-6.
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