miRTar: 快速而準確預測microRNA target之網站工具

Abstract

目前已經有很多microRNAs被發現，而且也進一步透過實驗驗證。針對找尋microRNA target，有許多的軟體被設計開發出來，例如miRanda、RNAhybrid、和TargetScan，但是，當使用這些軟體在大量的序列上，找尋microRNA target時是很耗時的，況且因為沒有很人性化的輸入查詢界面，對一個生物學家而言是非常不方便的。因此，為了幫助生物學家可以簡便的分析預測microRNA target，一個網頁工具是必要的。本研究主要的貢獻為設計一網站工具-miRTar，提供更人性化的界面引導使用者輸入自訂的microRNA序列或miRBase的microRNA ID，並在哺乳動物基因的保留序列上找尋出該microRNA的target。另一方面，我們也會提供mRNA上面有miRNA target site的RNA二級結構相關分析。miRTar設計的概念，主要是運用一個dynamic programming演算法的過濾步驟，再藉由miRanda、RNAhybrid和TargetScan來預測miRNA targets。經過與miRanda、RNAhybrid和TargetScan的效能評比，miRTar在效能方面有顯著的改進。miRTar網站目前建置在http://miRTar.mbc.nctu.edu.tw。

Numerous microRNAs (miRNA) have been identified and experimentally validated. For identifying miRNA targets, a variety of programs such as miRanda, RNAhybrid and TargetScan have been developed. However these tools are time-consuming and inconvenient for biologists when predicting miRNA targets in a large sequence database. In order to perform the analysis in a more convenient manner, a web-based tool for identifying miRNA targets is crucial. This work presents an efficient web server, namely miRTar, which utilizes an intuitive interface that allows users to input a user-defined miRNA sequence or accession numbers of the miRBase for identifying miRNA targets against the conserved sequences of mRNAs of mammalian genes. Furthermore, this work also provides additional information about the RNA secondary structures of the mRNA containing the miRNA target site, which can be targeted by miRNAs. The miRTar utilizes a filtering strategy, which was implemented based on dynamic programming, just before applying miRanda, RNAhybrid and TargetScan for miRNA target prediction. By comparing the proposed web server to miRanda, RNAhybrid and TargetScan, miRTar performs remarkably more efficiently than those software. This prediction web server is now available at http://miRTar.mbc.nctu.edu.tw/.