偵測核糖核酸 H 型偽結之研究

Abstract

已知在所有種類的核糖核酸序列中幾乎皆可找到所謂的偽結，在生物反應的過程中，這些偽結被認為扮演著重要功能性的角色。除此之外，目前大多數的核糖核酸偽結皆屬於 H 型。因此，偵測這些 H 型的偽結將有助於我們瞭解核糖核酸的結構及相關的功能。然而，現有的程式對於這種 H 型偽結的偵測仍然是相當費時，甚至有些時候其偵測出來的偽結是不正確的。因此，發展一個有效率且準確度高的工具來偵測 H 型的核糖核酸偽結是件值得研究的課題。在本論文中， 我們提出了一個啟發式的策略，並且根據這個策略發展出一個全新的工具 HPknotter 來正確而且有效率地偵測核糖核酸序列中的 H 型偽結。除此之外，我們也利用一些已知具有 H 型偽結的核糖核酸序列來測試並證明 HPknotter 的適用性及準確度。

RNA H-type pseudoknots are ubiquitous pseudoknots that are known to be found in almost all classes of RNA sequences and thought to play a functionally important role in variety of biological processes. Hence, detecting these RNA H-type pseudoknots will enhance our understanding of RNA structures and their associated functions. However, the currently existing programs for detecting such RNA H-type pseudoknots are still time-consuming and sometimes even ineffective. Therefore, efficient and effective tools for detecting the RNA H-type pseudoknots are needed. In this thesis, we propose a heuristic approach to develop a novel tool, called HPknotter, for accurately and efficiently detecting RNA H-type pseudoknots in a given RNA sequence. In addition, we demonstrate the applicability and effectiveness of our HPknotter by testing it on several RNA sequences with known H-type pseudoknots.