核醣核酸分子參與許多生物程序，如基因的調控與蛋白質的合成。研究功能性核醣核酸模體(functional RNA motif)可獲得有用之資訊於瞭解核醣核酸之調控機制。近年來，許多資料庫累積了各種不同類型功能性核醣核酸模體之資料，並有許多計算方法被建立使用於分析核醣核酸序列中之功能性核醣核酸模體。然而，目前仍缺乏一個整合性系統，將這些資料與分析方法整合在一起，以提供使用者一個綜合性分析流程於探索功能性核醣核酸模體。本研究目的即是設計與實作一個整合性網頁介面系統—fRNAfinder，以幫助使用者便利地與廣泛地研究分析核醣核酸序列中之功能性核醣核酸模體。此系統提供了三種主要功能：一、辨識輸入核醣核酸序列中之已知功能性核醣核酸模體之相似物；二、發現輸入核醣核酸序列中之保留性核醣核酸模體；三、搜尋使用者描述之核醣核酸模體之相似物於數個核醣核酸序列資料庫。此系統整合了各種相關資料與分析方法，並建立了一個容易使用之網頁介面，讓使用者不需下載安裝，即可方便地使用各種分析程序。此外，本研究開發了三個新穎的方法—RiboSW、RNALogo、RNAMST並整合於此系統之中，以增進此系統分析與呈現之能力。RiboSW能有效地辨識核醣核酸序列中之riboswitches；RNALogo能良好地呈現結構性核醣核酸模體之特性；RNAMST能快速有效地搜尋使用者描述之核醣核酸模體之相似物於數個核醣核酸序列資料庫之中。此系統之預測結果皆以良好的圖形視覺化方式呈現於網頁上。因此，我們認為此系統將有助於使用者方便地與廣泛地分析核醣核酸序列中之功能性核醣核酸模體。 RNA molecules are involved in numerous biological processes, ranging from gene regulation to protein synthesis. Researching into the functional RNA motifs can obtain useful information for deciphering RNA regulatory mechanisms. Various databases and web servers have accumulated functional RNA motifs during the last few decades, and several approaches have been developed for computational analysis of functional RNA motifs against RNA sequences. However, there is lack of a system integrating these data sources and analytical approaches for comprehensive analysis of functional RNA motifs against RNA sequences. Therefore, we propose an integrated web-based system, fRNAfinder, to facilitate user conveniently and comprehensively analyzing functional RNA motifs against RNA sequences. Though our easy-to-use web server, user can conveniently identify homologs of various known functional RNA motifs against an input RNA sequence, discover conserved RNA motifs against input RNA sequences, and search user-specified RNA motif against numerous RNA sequence databases. Various analytical approaches and data sources were incorporated into fRNAfinder. User can conveniently use these programs without having to download the code and get the programs to run. In addition, three novel approaches, RiboSW, RNALogo and RNAMST, were developed and incorporated to enhance ability of fRNAfinder. RiboSW can efficiently and conveniently identify riboswitches within RNA sequences. RNALogo provides a new graphical representation of the pattern in structural RNA motifs. RNAMST can efficiently and flexibly search user-specified RNA motif against RNA databases. The predictive results and related information are presented with good graphical visualization on fRNAfinder web page. Thus, we suggest that the fRNAfinder is a useful web server which facilitates user conveniently and comprehensively analyzing functional RNA motifs against RNA sequences. 研究期間：10008 ~ 10107
