RNA分子已知在細胞中扮演多種重要的角色。基本上，RNA的功能主要取決於它的三級結構。有愈來愈多的RNA三級結構被加入PDB的資料庫，因此一個能夠快速且準確地搜尋PDB資料庫以找出相似RNA三級結構或子結構的生物資訊工具是有助於我們了解RNA結構與功能的關係。自2011年首次發表以來，R3D-BLAST已經成為一個搜尋PDB資料庫中相似的RNA結構與子結構的有用工具，它是利用structural-alphabet (SA)的方法實做出來的工具，這個方法利用23個結構字母將RNA的三級結構編碼成為一級帶有SA字元的序列，並且使用BLAST來搜尋這些SA-encoded序列以找出相似的RNA三級子結構。在本研究中，我們使用具代表性且無多餘的RNA三級結構來建構出一個新的且品質更高的SA，並根據這個SA來重新實做R3D-BLAST成為一個新的網站伺服器並命名為R3D-BLAST2。除此之外，我們修改了R3D-BLAST2的核心程式使它可以接受mmCIF格式的RNA三級結構做為輸入。最後，根據我們用測試資料組做實驗的結果顯示出R3D-BLAST2確實能比以前的版本R3D-BLAST以及其它類似的RNA結構搜尋工具RNA FRABASE、FASTR3D以及RAG-3D找出更多和query RNA結構相似的RNA三級子結構。因此，我們相信R3D-BLAST2可以做為一個有價值的BLAST-like搜尋工具能夠更精準地搜尋出PDB資料庫中相似的RNA三級子結構。

RNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D structures are deposited in the Protein Data Bank (PDB), a bioinformatics tool that can quickly and accurately search the PDB database for similar RNA 3D structures or substructures is helpful to understand the structural and functional relationships of RNAs. Since its first release in 2011, R3D-BLAST has become a useful tool for searching the PDB database for similar RNA 3D structures and substructures. It was implemented by a structur-al-alphabet (SA)-based approach, which utilizes an SA with 23 structural letters to encode RNA 3D structures into 1D sequences of SA letters and applies BLAST to the SA-encoded sequences for searching similar RNA 3D substructures. In this study, we have re-implemented R3D-BLAST into a new web server named R3D-BLAST2 based on a higher quality SA newly constructed from a representative and sufficiently non-redundant list of RNA 3D structures. In addition, we have modified the kernel program in R3D-BLAST2 so that it can accept as input an RNA 3D structure in the mmCIF format. Our experimental results on a benchmark dataset have finally shown that R3D-BLAST2 indeed outperforms its previous version R3D-BLAST and other similar tools RNA FRABASE, FASTR3D and RAG-3D by searching a larger number of RNA 3D substructures similar to those of the query RNA. Therefore, we believe that R3D-BLAST2 can serve as a valuable BLAST-like search tool that can more accurately search the PDB database for similar RNA 3D substructures.

中文摘要----------------------------------I
Abstract--------------------------------II
Acknowledgement------------------------III
Contents--------------------------------IV
List of figures--------------------------V
List of tables--------------------------VI
Chapter 1 Introduction------------------1
Chapter 2 Implementation----------------3
2.1 Method of R3D-BLAST2-----------------4
Chapter 3 Results and Discussion-------11
3.1 Dataset and parameters--------------11
3.2 Experimental results----------------12
3.2.1 Comparison of search results------12
3.2.2 Comparison of running time--------14
Chapter 4 Conclusion-------------------16
References------------------------------17

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