分散式重複序列資料庫之效能評估

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姓名

張祜嘉(Hu-Chia Chang) 查詢紙本館藏

畢業系所

資訊工程學系

論文名稱

分散式重複序列資料庫之效能評估
(Performance Evaluation of A Distributed Database of Repetitive Elements in Complete Genomes)

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摘要(中)

前一版的重複序列資料庫是建立在集中式資料庫系統上的，此資料庫目前包含了大量的資料，而生物資訊的資料也日漸擴增，重複序列資料庫的效能成為很重要的問題。為了得到更好的效能，我們建立了分散式重複序列資料庫。在分散式資料庫上，資料分散的方法是平衡負載的重要機制。我們設計了許多資料分散的方法來做實驗以得到最適合重複序列資料的方法，也發展了智慧型元件來輔助我們的系統以得到更好的效能。

摘要(英)

The original version of Repeat Sequence Database (RSDB) was created based on centralized database systems (CDBSs). It contains large number of data currently, and the size of biological data is increasing rapidly. The performance of RSDB becomes an important issue. Distributed RSDB (DRSDB) is created based on distributed database systems (DDBSs) in order to obtain better performance. Data distribution serves as an important load-balancing mechanism. We design lots of data distribution approaches and try to find the proper approaches to our particular system with experiments. The results show that query processor does not always choose the right data access paths for queries, and we develop an intelligent component to assist our system executing queries wisely in order to obtain much better performance.

關鍵字(中)

★ 資料庫
★ 重複序列
★ 分散式

關鍵字(英)

★ Database
★ Complete Genomes
★ Repetitive Elements
★ Performance Evaluation
★ Distributed

論文目次

Contents......................................................................................................i
List of Figures...........................................................................................iii
List of Tables...............................................................................................v
Chapter 1 Introduction................................................................................1
1.1 Motivation.....................................................................................2
1.2 Goal and Purpose..........................................................................2
1.3 Related Work.................................................................................2
1.4 Organization of This Thesis..........................................................3
Chapter 2 Repeat Sequence Database.........................................................5
2.1 System Architecture......................................................................5
2.2 Queries on RSDB.........................................................................6
Chapter 3 Experimental Design................................................................12
3.1 Experimental Environment.........................................................12
3.2 Index strategies for DRSDB.......................................................12
3.3 Data Distribution.........................................................................14
3.4 Experimental Queries.................................................................17
Chapter 4 Performance Evaluation...........................................................20
4.1 Search By Feature.......................................................................20
4.2 Search By Range.........................................................................26
4.3 Search By Pattern........................................................................30
4.4 Search by Accession Number/Sequence ID...............................33
4.5 Experiments on Other Organisms...............................................33
4.6 Concurrent Requests...................................................................33
4.7 The Intelligent Component.........................................................36
i
Chapter 5 Discussion and Conclusion......................................................37
References.................................................................................................39
Appendix...................................................................................................41
ii
List of Figures
Figure 1. The relationship among three tables............................................5
Figure 2. System architecture of RSDB.....................................................6
Figure 3. Fields in Search By Feature web page........................................7
Figure 4. Search By Feature results............................................................9
Figure 5. Specify begin and end position in Search By Range web page..9
Figure 6. The number of identical repeats and repeat copies are shown in the result page...........................................................................................10
Figure 7. Search By Repeat Pattern web page..........................................11
Figure 8. RSDB returns 277 patterns matching user queries...................11
Figure 9. System architecture of DRSDB................................................12
Figure 10. Data structure of Trie for Search By Pattern...........................13
Figure 11. Distribution by interleaving with each accession number......14
Figure 12. Distribution by interleaving with each value of pos_begin or chromosome..............................................................................................15
Figure 13. Distribution by interleaving with each record of a column value..........................................................................................................16
Figure 14. Distribution by statistics in RSDB’s data warehouse..............17
Figure 15. Comparison among different indexes of Query 6...................20
Figure 16. Experimental results of Search By Feature in CDBSs............21
Figure 17. Comparison between CDBSs and DDBSs of Query 1...........22
Figure 18. Comparison between CDBSs and DDBSs of Query 7...........23
Figure 19. Comparison between CDBSs and DDBSs of Query 3...........23
Figure 20. Comparison between CDBSs and DDBSs of Query 2...........24
Figure 21. Comparison between CDBSs and DDBSs of Query 6...........24
iii
Figure 22. Comparison between CDBSs and DDBSs of Query 4...........25
Figure 23. Comparison between CDBSs and DDBSs of Query 5...........25
Figure 24. Experimental results of Search By Range in CDBSs.............26
Figure 25. Comparison between CDBSs and DDBSs of Query 1...........27
Figure 26. Comparison between CDBSs and DDBSs of Query 2...........28
Figure 27. Comparison between CDBSs and DDBSs of Query 3...........28
Figure 28. Comparison between CDBSs and DDBSs of Search By Range...................................................................................................................29
Figure 29. Comparison among queries using different range interval.....29
Figure 30. Experimental results in CDBSs of Search by Pattern.............30
Figure 31. Experimental result of pattern with or without ‘?’..................31
Figure 32. Comparison between different index approaches...................32
Figure 33. Comparison among three index methods................................32
Figure 34. Concurrent Requests of Search By Feature............................34
Figure 35. Concurrent Requests of Search By Range..............................35
Figure 36. Concurrent Requests of Search By Pattern.............................35
iv
List of Tables
Table 1. The amount of data in RSDB........................................................5
Table 2. Available options for fields...........................................................8
Table 3. Queries used to evaluate Search by Feature...............................18
Table 4. Queries used to evaluate Search By Range................................18
Table 5. Queries used to evaluate Search By Pattern...............................19
Table 6. Queries used to perform simulations..........................................19
Table 7. Experimental results of Search By Feature when the data size is 24.7M records...........................................................................................21
Table 8. Experimental results of Search By Range when the data size is 85.1M records...........................................................................................27
Table 9. Comparison amongs three index methods..................................31
Table 10. Experimental Results of Search By Pattern using Trie.............32
Table 11. Experimental result of Search By AC/ID..................................33
Table 12.The amount of identical repeats for each organism...................41
Table 13. The amount of total repeat copies for each organism...............42
v

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39
and Humans, 28. 288-305.

指導教授

洪炯宗(Jorng-Tzong Horng)

審核日期

2003-3-5

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