結論與未來方向 - 利用圖形表示的基因規劃法找尋核醣核酸的共同結構元

5.1 結論

本系統建立了一種新的描述語言來描述核醣核酸的二級結構，利用現有的二級結構預測工具提供能量資訊，使用基因規劃法來來尋找一群具有相同功能核醣核酸的共同結構元，不需要有序列排比的資訊，直接以二級結構作為搜尋的目標，降低系統搜尋空間。

而系統的描述語言以圖形表示，對於一條莖幹的兩股間距離很長時，本系統亦有可能找到此莖幹，但其表現能力尚不強，系統仍較為偏好距離較近的莖幹。

若要強化此功能，則容易影響到搜尋一般的莖幹，這在需要參數設定上做選擇或調整。

我們使用基因規劃法搜尋核醣核酸的共同結構元，由實驗結果可以看出基因規劃法能避開大量雜訊的干擾，而在不會花費太多時間的情況下尚能找到還不錯的結果。

5.2 未來研究方向

在進行研究的過程中，發現尚有一些研究方向可以延伸。

5.2.1 處理共同結構元莖幹數較多之家族

在我們的實驗中，對於共同結構元莖幹數較多的 RNaseP(high)資料，我們可以找出其真實共同結構元的子結構，經由簡單的測試，我們使用 FGGP 找出預測共同結構元後，先在每條序列上移除此共同結構元，然後再重複呼叫 FGGP，如此重複，可以漸漸提高 Matthews 相關係數。但是重複進行 FGGP，會漸漸增加雜訊，之後則使預測能力愈來愈差。

因此我們可以研究如何設定一個機制，判斷該重複呼叫幾次才是最好的，以及每次重複進行 FGGP 前該如何去掉多餘的雜訊，移除預測共同結構元後該如何處理，還有重複呼叫亦可以改為遞迴式的呼叫等，這些還有很多的研究空間，。

5.2.2 對多個家族做分群

我們以兩個家族混合資料丟入 FGGP 測試，當兩個家族結構元差異性很大時，有可能將一個家族的大部份序列取出來，因而達到了分群的目的。當家族的結構元差異性不是很大時分群的效果就不是很明顯，但可以調整某些參數可以使此能力稍微加強，因此我們可以朝著分群的方向繼續研究。

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在文檔中利用圖形表示的基因規劃法找尋核醣核酸的共同結構元 (頁 54-59)