結合基因演算法與模擬退火法於多重DNA序列之比對

Combination of GA and SA for Multiple DNA Sequence Alignment

10.6220/joq.2014.21(5).01

葉進儀(Jinn-Yi Yeh)；林軒仲(Syuan-Jhong Lin)

序列比對 ； 多重序列比對 ； 基因演算法 ； 模擬退火法 ； sequence alignment ； multiple sequence alignment ； genetic algorithms ； simulated annealing

品質學報

21卷5期（2014 / 10 / 31）

305 - 328

繁體中文

序列比對是將蛋白質中的基因或氨基酸進行對齊的動作，藉此找出兩序列的相似程度，而多重序列比對則是同時比對多個DNA或蛋白質序列，找出此序列群組中最佳的比對結果，本研究結合基因演算法及模擬退火法，先利用基因演算法物競天擇的概念，隨著世代演進逐漸產生近似最佳解，再利用模擬退火法進行小區塊內之比對修正，實驗結果顯示，利用基因演算法與模擬退火法之結合，使得基因演算法在跳脫局部最佳解的時候能有更大空間移動，而且也讓模擬退火法能有效解決經由基因演算法初步比對之後所產生的不良區域，此結合之序列比對結果比任何單一演算法的結果好，因此可以提升整體比對表現，將來能夠為生物學家在判斷未知序列功能時提供適當的輔助。

There was more and more DNA and protein sequence has been founded. The similar DNA sequence or protein sequence may have the same features. Therefore, sequence alignment has become the most popular technology in the field of bioinformatics. In this work, the combination of genetic algorithms and simulated annealing is used for multiple sequence alignment. Genetic algorithms apply the concept of fittest with evolution generation to gradually produce near optimal solutions. Simulated annealing is used to correct the alignment in small blocks. Experimental results show that the proposed method can let genetic algorithms' solutions to escape local optimum and to have more space to move, and also let simulated annealing effectively solves the problems with bad initial solutions generated by genetic algorithms. The results obtained by the proposed method are better than the results of any single algorithm. Therefore, the proposed method can improve the overall ratio of performance and will be able to provide appropriate support to biologists in determining the function of unknown sequence.

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