矩形樹語法是一種用來預測核糖核酸二級結構的演算法，近年來，核糖核酸二級結構預測一直都是熱門關注的問題，原因在於核糖核酸的結構對於核糖核酸的功能性有很大的關聯，例如核糖體移碼、核糖核酸的轉譯和複製。矩形樹語法提供一個可以建構出所有Rfam資料庫中所存在核糖核酸結構的優良方法，這是現有已提出的演算法中仍然無法做到的，尤其是其中一個稱為three-crossing的特殊結構。為了展現出矩形樹語法的優點，它仍然需要一個圖形化、友善且容易使用的介面來表現它，因此我們根據這個目標建立一個名字叫做WebRTG的網站，它提供一個簡化的輸入和圖形化的輸出功能，另外也客製化讓使用者可以上傳自己的資料來改善結構預測結果，在這篇論文中，我們將介紹矩形樹語法的功能性，以及WebRTG介面實作的細節。

The Rectangle Tree Grammar (RTG) algorithm is a method for generic RNA secondary structure prediction. Though the flexibility brought by this algorithm is tremendous, a visualized, user-friendly, and easy-to-use interface is still in need. For this purpose, we have built a web-based interface, WebRTG, which simplies the input and visualizes the output of the RTG algorithm. In this thesis, we shall describe the functionality of the RTG algorithm, as well as the implementation details of the WebRTG interface.

1. Introduction 1
2. WebRTG - From User's Point of View 4
2.1 Input of WebRTG..............................5
2.1.1 Format of Input Sequence...............5
2.1.2 Format of Training Data................5
2.1.3 Customizing Training Data..............6
2.1.4 Submitting Task........................7
2.1.5 Quick Submission for Anonymous Users...8
2.2 Output of WebRTG.............................9
2.2.1 Viewing Prediction Result..............9
2.2.2 Storing the Result....................10
3. WebRTG - Design Issues 12
3.1 Input Interface.............................12
3.2 Data Validation.............................13
3.3 Task Queuing System.........................14
3.4 Output Interface............................17
3.5 Workload Forecasting........................18
4. Conclusion and Future Work......................19

[1] crond(8) - Linux man page. http://linux.die.net/man/8/crond.
[2] Fiddler: The Free Web Debugging Proxy for Any Browser, System or Platform. http://www.telerik.com/fiddler.
[3] Github: PHPMailer. http://www.telerik.com/fiddler.
[4] Markup Validation Service. https://validator.w3.org/.
[5] rfam: RNA Families Database. http://rfam.xfam.org/.
[6] Stochastic Context-Free Grammar. https://en.wikipedia.org/wiki/Stochastic_context-free_grammar.
[7] The Dot Bracket File Format. http://rna.urmc.rochester.edu/Text/File_Formats.html.
[8] VARNA: Visualization Applet for RNA. http://http://varna.lri.fr/.
[9] WebRTG: A Web Front-end for RNA Structure Prediction using Rectangle Tree Grammar. http://ada.cs.nthu.edu.tw/web-genome.
[10] Wikipedia: A List of RNA Structure Prediction Soft-ware. https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software.
[11] Wikipedia: JavaScript. https://zh.wikipedia.org/wiki/JavaScript.
[12] M. Li, M. Cheng, Y. Ye, W. K. Hon, H. F. Ting, T. W. Lam, C. Y. Tang, T.Wong, and S. M. Yiu. Predicting RNA Secondary Structures: One-Grammar-Fits-All Solution. In International Symposium on Bioinformatics Research and Applications (ISBRA), pages 211{222, 2015.