病毒分類之研究-藉由基因體編碼序列

傳統的病毒分類方法是根據型態學、核酸型態(DNA 或RNA) 、核酸是單鏈/雙鏈、或病毒入侵的物種。本研究從基因體的觀點, 根據編碼序列(CDS) 來做病毒分類。其中CDS 是用來定義蛋白質的編碼區域。根據『相似的CDS之轉譯序列擁有相近的生物功能』的簡單假設, 我們以E-value(E)值為評量標準, 利用blast 程式將CDS 序列分成不同的群組, 然後根據這些群組, 將病毒轉換成具有代表性的向量, 以便做進一步分類處理。實驗資料來源是選擇過的22科(family) 病毒, 包含1,596種病毒。利用著名的SVM 分類器,經由5-fold 交叉驗證, 當E-value 值為39時, 得到最佳的正確率為93.8% 。本研究對於比較基因體研究提供一個新的病毒分類方法。

關鍵字

病毒分類；編碼序列；比較基因體研究

並列摘要

Traditional approaches for virus classification based on morphology, the type of nucleic acid genome (DNA or RNA), the nucleic acid being single/double stranded, or the species the virus invaded. In this study, from the genomic point of view, we have virus classification via translated coding sequences (CDS). Note that the translated CDS feature is used to define a protein coding region. Under an assumption, for simplicity, that similar translated CDS sequences conserve similar biological functions, the translated CDS sequences were clustered into distinct groups via a criteria of the E-value(E) of blast program such that the instances of viruses could be transferred into representative vectors for further classification processes. The experimental resources included 22 virus family consisting of 1,596 viruses. The best accuracy was as high as 93.8% when E=39 achieved by the well known SVM classifier through 5-fold cross-validation. This study provided a new approach to virus classifiation for comparative genomic analysis.

並列關鍵字

virus classification ； translated coding sequence ； comparative genomic analysis

參考文獻

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國際替代計量

病毒分類之研究-藉由基因體編碼序列

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