臺灣博碩士論文加值系統

　　根據KEGG所定義的代謝參考路徑，我們提出一個方法去比較不同物種，其代謝路徑之間的差異以及相似性。透過一百多個路徑同時比較的結果，可以幫助研究人員們去了解代謝路徑的演化以及adaptation等過程。比較的結果不但可以用來檢驗基因體註解的結果之外，同時也能夠去鑑定可能失去的基因以及尋找替代路徑等應用。
　　在此篇論文中，我們採用我們所開發出來的程式，去比較弧菌之間的差異性。我們拿了V. cholerae、V. vulnificus CMCP6以及V. parahaemolyticus分別去對V. vulnificus YJ016去做比較。沒錯，比較的結果的確吻合現今對弧菌屬在演化上的關係。也就是說，V. vulnificus YJ016與V. vulnificus CMCP6最為相似，其次是V. parahaemolyticus，最後才是V. cholerae。更進一步地，我們發現在碳水化合物相關的代謝中主要有兩個代謝路徑在弧菌屬中差異性很大，分別是citrate 的循環以及galactose的代謝。文中的最後，探討弧菌屬在碳水化合物相關的代謝路徑上之差異性以及說明代謝路徑比較分析方法有哪些其他的應用，期望能夠對於瞭解物種之間的相似性以及差異性之研究方式能有貢獻。為了提昇整個研究的可用性以及價值，我們的CAMP (Comparative Analysis of Metabolic Pathway) 系統將提供給學術單位以及非營利的研究機構免費使用，網址在http://gel.ym.edu.tw/camp。

We present a systematic method for comparing the metabolic pathways (pathways for short) of different organisms based on KEGG reference pathway data. Our comparison of over 100 pathways simultaneously can help researchers to unravel what have happened during the course of evolution and adaptation in each well-defined pathway. The comparison results can also be used to improve the genome annotation results by either identifying missing genes, finding alternative routes or reducing annotation errors.
In this study, our method was applied to compare the Vibrio species (V. cholerae, V. vulnificus CMCP6 and V. parahaemolyticus) against Vibrio vulnificus YJ016 among 112 metabolic pathways. The results are consistent with the phylogenetic analysis results currently available, i.e. V. vulnificus YJ016 is much similar to V. vulnificus CMCP6, than with V. parahaemolyticus and V. cholerae. We also found two carbohydrate related pathways that are quite different among these Vibrios. They are citrate cycle and galactose metabolism. The differences between these Vibrio pathogens in carbohydrate metabolism are further investigated, which can yield a more comprehensive understanding of the similarities and differences between the organisms. The possible applications of our MPC (metabolic pathway comparison) method are discussed. The CAMP (Comparative Analysis of Metabolic Pathways) system will be freely available for academic or nonprofit use at http://gel.ym.edu.tw/camp.

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