水稻表現序列標幟(EST)功能分析自動化系統

Rice Expressed Sequence Tag (EST) Automated Functional Analysis System

呂秀英(Hsiu-Ying Lu) ； 陳政道(Cheng-Tao Chen) ； 呂椿棠(Chun-Tang Lu) ； 邱怡嘉(Yi-Chia Chiu) ； 魏夢麗(Meng-Li Wei)

《台灣農業研究》 57卷2期 (2008/06) Pp. 103-118

https://doi.org/10.6156/JTAR/2008.05702.03

摘要

表現序列標幟(expressed sequence tag, EST)是cDNA序列片段，直接研究EST可獲取基因表現訊息。透過EST的功能註解、分類和表現量統計，能瞭解不同cDNA基因庫間之基因表現型式的差異性及表現基因的功能類別。現存於公共資料庫的水稻EST序列數量相當龐大，可作爲水稻基因組功能註解的重要資源。但針對這些巨量EST，僅靠人工是不可能在短時間內完成所有分析與計算。因此，本研究在Linux伺服器以MySQL資料庫管理系統建立本地資料庫，並綜合Perl和PHP程式語言之運用，成功研發了一套完整的水稻EST功能分析自動化系統，能快速且準確完成EST功能註解、分類及表現量統計的全程分析工作，大大提高了工作效率。使用者無須登錄到Linux分析平台，只要在Microsoft Window操作環境下透過網頁瀏覽器，即可直接使用該系統。系統以Web界面爲基礎所設計的輸入畫面在操作上非常簡便，且分析完成後主動將輸出結果透過電子郵件寄給使用者。本系統亦可容易地擴展運用到其他物種之EST功能分析工作，對分子遺傳實驗室發展EST分析工作具有重要意義。

關鍵字

水稻 ； 表現序列標幟 ； 功能註解及分類 ； 基因表現量統計 ； 自動化系統 ； Perl語言

並列摘要

Expressed sequence tag (EST) is the fragment of cDNA sequence. Direct study of EST is therefore helpful to obtain the gene expression information. The analytical procedures of EST functional annotation, classification and representation statistics are used to detect the differences in gene expression patterns among libraries and identify the functional categories involved. A vast number of rice (Oryza sativa L.) EST sequences in the public databases provide an important resource for functional annotation of rice genome. However, it's impossible to accomplish the entire process of functional analysis for large-scale EST sequences within a short time using manual intervention only. To accelerate the functional analysis for rice EST sequences, an automated system was constructed by using Perl and PHP scripts based on a local MySQL database of the Linux platform. A series of analysis including functional annotation, classification and representation statistics for EST sequences could be done automatically, which provides a rapid, accurate and efficient tool for large-scale rice EST functional analysis. The system could be used directly through a web browser on Microsoft Window operating system without logging into the Linux platform. The web-based input interface of automated system is very easy and convenient for use. After finishing the work, an email message with output results was created and sent to users. The automated system could also be easily expanded and implemented in the EST functional analysis of other species, which facilitates the EST analysis in molecular genetics laboratories.

並列關鍵字

Rice Oryza sativa L. ； Expressed sequence tag ； Functional annotation and classification ； Gene representation statistics ； Automated system ； Perl script