Ribonucleic acid (RNA)在細胞內不僅是基因傳訊者，更以small regulatory RNA (如piRNA、miRNA、siRNA等)的形式調節著其他RNA (target RNA)，進而影響許多基因表現，在細胞生長、凋亡、分化等機制中扮演著重要角色，因此熟知RNA的調控功能可幫助我們探索更多的生物機能，進而應用在生物醫學等方面。
傳統上想知道某個(regulatory RNA)-(target RNA)對的關係，就需進行一次實驗，若想探討多組RNA-RNA對，則會耗費許多時間與精力。2011年CLASH (Cross-linking ligation and sequencing of hybrids)這個實驗技術被提出，能大量有效獲取含有(regulatory RNA)-(target RNA)對的read，然而由於實驗過程中的不完美，含有(regulatory RNA)-(target RNA)對的CLASH read只佔少數，更不知read上對應的regulatory RNA與target RNA的身分和真實結合情況，為此需要進行後續的生物資訊分析，才能辨識出read中所隱含的regulatory RNA及target RNA的身分。
目前文獻中有三種分析方法(piRTarBase, Hyb, CLAN)可對CLASH實驗得到的read進行分析，然而三種分析方法各有優缺點以及不同的設計流程，還須要使用者熟悉Command-Line Interface (CLI)才能進行安裝與操作，並且三種分析方法最後都只給出read上regulatory RNA與target RNA的身分，沒有進一步分析兩者可能的結合區域和結合穩定度。另外也沒有整理出真正對生物學家有幫助的資訊，例如:一個regulatory RNA可以調控那些target RNA以及一個target RNA會被那些regulatory RNA調控等。因此本研究對於這三種分析方法進行整合與改良，開發出一個更完整的網頁分析平台，能讓生物學家只需上傳資料不需操作Command-Line Interface便能進行分析，並提供多種資訊查詢與輔助參照，以及將分析結果進行統整與視覺化呈現，方便生物學家觀察。
最後本研究利用開發出的網頁分析工具，針對十組CLASH資料集進行分析，探討三種分析方法的異同，以及平台所設計參數的作用，總結出推薦的分析方式。

RNA interference (RNAi) plays an important role in post-transcriptional regulation of gene expression. The CLASH (Cross-linking, Ligation and Sequencing of Hybrids) technique can efficiently captures reads which contain information of (regulatory RNA)–(target RNA) interactions by physically joining two RNAs. Nevertheless, the number of reads containing information are relatively rare; moreover, these reads do not provide the identity of regulatory RNA and target RNA. Therefore, the follow-up bioinformatics analysis is required. At present, there are three analysis methods (piRTarBase, Hyb, CLAN) can analyze the reads obtained from the CLASH experiment. However, each of the three analysis methods has advantages and disadvantages as well as different design processes. All of them require biologists to be familiar with the command line interface (CLI) to install and operate. Furthermore, the result of three analysis methods only gives the identity of the regulatory RNA and target RNA on the read, without further analysis of the possible binding site and binding stability of the two RNAs. As mentioned above, we present a more complete analysis process web tool that allows biologists to analyze data without using CLI, have a variety of information to query, and easily make an observation by visualizing the analysis results.

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