基於基因本體論之簡單重複序列間區域搜尋系統

分子生物標記是指在生物體中可以用來對特定目標性狀進行特徵標識或區別不同物種、品系、或個體的分子組成。本研究的主要目標是如何透過既有模式物種的基因體序列與標註資訊，發掘某特定目標性狀或生物功能相關的生物標記，特別是由簡單重複序列間區域（Inter- Simple Sequence Repeat, ISSR）所構成的多型性分子標記。在各種生物的基因體中存在大量的簡單重複序列（SSR），因此透過設計由一對SSR組成的ISSR分子標記，並指定該組SSR為聚合酶連鎖反應實驗（Polymerase Chain Reaction, PCR）之兩端的引子（Primer），可以快速擷取座落在這對SSR之間不同長度及內容的基因片段，再透過跨不同物種或不同品系實驗樣本的電泳分析實驗辨識該ISSR分子所框限的序列片段是否具多型性來決定該分子是否適合作為目標性狀的有效生物標記。本論文完成一套基於權重式基因本體論（Gene Ontology）的計算方式，由使用者輸入與特定功能相關的關鍵字，系統自動計算分析與該特定功能或目標性狀相關之基因群組，再由這些候選基因分析目標物種所有可能的ISSR生物標記。

關鍵字

分子生物標記；簡單重複序列間區域；功能基因群組；權重式基因本體論

並列摘要

Molecular markers within organisms can be applied as specific target traits for distinguishing various species, strains, or individuals. In this paper, we developed an online web tool and database for discovering functional molecular markers of specified target traits based on annotated genomics of selected model species, especially focusing on inter-simple sequence repeat (ISSR) biomarkers. Simple sequence repeats appear highly abundant in all different kind of organisms, and distribute in both intergenic and genetic regions. Assigning a pair of SSRs as both ending primers for polymerase chain reaction experiments, various segment lengths and contents within the pair of SSRs could be retrieved efficiently for comparison. Through electrophoretic analysis on samples from different species, strains, and individuals, polymorphisms of segmented sequences from the ISSR markers could be decided for its suitability as an effective biomarker. To achieve this goal, we have designed a system based on weighted Gene Ontology annotation analysis for selecting functional gene clusters. After users providing query functional keywords, the system automatically responds a set of functional genes and their corresponding ISSR markers.

並列關鍵字

molecular marker ； inter-simple sequence repeat (ISSR) ； functional gene cluster ； weighted gene ontology

國際替代計量

基於基因本體論之簡單重複序列間區域搜尋系統

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