Journal of Taiwan Agricultural Research

Author:Hsiu-Ying Lu, Cheng-Tao Chen, Chun-Tang Lu*, Yi-Chia Chiu, and Meng-Li Wei

Abstract:

    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.

Key words:Rice (Oryza sativa L.), Expressed sequence tag, Functional annotation and classification, Gene representation statistics, Automated system, Perl script

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