蘭科植物是被子植物中的第二大科，是最具多樣性，分布最廣的植物。蝴蝶蘭在臺灣也有著很高的經濟價值。因此研究蘭科植物基因的調控或是鑑定蘭科植物的蛋白質家族十分重要。而蘭花基因資料庫(Orchidbase)第五版目前收錄五種蘭科植物的全基因組序列，可以供生物學家查詢解序後的資料。本研究除了在Orchidbase新增兩個舌唇蘭物種外，也開發三個功能，分別是Enhanced sequence search、Domain Search、Promoter Analysis。本研究開發之第一個功能Enhanced sequence search功能提升原本OrchiBase的BLAST功能。在BLAST分析後增加基因表現量之圖表製作，其中包含熱圖(heat map)、集群(cluster)、表現圖譜(expression pattern)及主成分分析(Principal component analysis, PCA)之功能，將表現量的數字資料圖形化(data visualization)，可快速提供使用者理解這些蘭科植物基因表現資料背後所代表的科學意義。可以讓生物學家對於蛋白質家族在蘭科植物的基因數量及其親緣演化關係有著一定可信度的預測。生物學家也可以用本研究開發的第二個功能，Domain Search，用蛋白質結構域(domain)的角度來預測同源基因。可以彌補用Enhanced sequence search功能中找到的同源基因數量不足的缺點。而第三個功能為Promoter Analysis，提供給生物學家查詢蘭花基因啟動子可能結合的轉錄因子，也提供生物學家對於有興趣的基因的上游調控機制有更進一步的了解。

The Orchidaceae are a diverse and widespread family of flowering plants, and Phalaenopsis also hase high economic value in Taiwan. Therefore, it is very important to study the regulation of genes in orchids or to identify the protein family of orchids. The fifth version of Orhidbase (Orchidbase 5.0) currently contains the entire genome sequences of five orchid species, which can be used by biologists to inquire about the data of genome sequencing. In addition to adding two new Platanthera species in Orchidbase, this research also developed three website functions. They are respectively Enhanced sequence search, Domain Search, and Promoter Analysis. The first function of this study, Enhanced sequence search, enhances the original BLAST function of OrchiBase. After BLAST analysis, it increases the gene expression graph, which includes heat map, cluster, expression pattern and principal component analysis (PCA). These data visualization of expression data can quickly provide users with an understanding of the scientific significance behind these orchid plant gene expression data. They also provide biologists to have a certain credibility in predicting the gene numbers of the protein family in orchids and their genetic evolution. Biologists can also use the second function in this research, Domain Search, to predict homologous genes from the perspective of protein domains. It can make up for the shortcomings of insufficient number of homologous genes found in the Enhanced sequence search.The third function is Promoter Analysis, which provides biologists with inquiring about the transcription factors that orchid gene promoters may bind, and also provides biologists with a better understanding of the upstream regulatory mechanism of genes of interest.

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