IntroductionFunctional genomics is defined as the use of molecular biology tools to explore the functions and interactions of genes based on genome sequencing data (SERC, 2013). Expressed sequence tag (EST) and serial analysis of gene expression (SAGE) are among the commonly used techniques in functional genomics. The goal of transcriptome studies is to identify transcripts expressed in a genome. Since studies of the human genome, EST has been the primary technique used for transcript identification. Recently, SAGE has been widely used in transcriptome analysis. ESTs are short, single-pass, randomly selected cDNA sequences derived from library clones (Nagaraj, Gasser, & Ranganathan, 2006). SAGE is a quantitative and direct method for analyzing gene expression without prior knowledge of genes (Yamamoto, Wakatsuki, Hada & Ryo, 2001). Although EST and SAGE are applied to the study of functional genomics, their approaches are different. Sun et al. (2004) stated that the EST method is based on a single transcript, single clone, single sequencing approach, while SAGE is based on multiple transcripts, multiple tags, single clone, and single sequencing approach, resulting in each SAGE sequence representing multiple transcripts. Basic principles of EST and SAGENagaraj et al. (2006) mentioned that EST analysis involves several steps and there are various tools available to obtain biological information from the analysis. The basic principles of EST are messenger RNA (mRNA) sequences to represent duplicates of expressed genes, cDNA libraries created from various cells and tissues, single-pass sequencing of both ends of inserting and accumulating a readable sequence portion in the EST database. In order to generate the EST, RNAs are first reverse transcribed...... middle of article ......gs in Bioinformatics, 8(1), 6-21.Patino, WD, Milan , OY and Hwang, PM (2002). Serial analysis of gene expression. Circulation Research, 91, 565-569. Science Education Resource Center. (2013). Functional genomics: strategies for testing and extending genomic data in the laboratory. Retrieved from http://serc.carleton.edu/exploring genomics/chamaecrista/function_geno.html. Sun, M., Zhou, G., Lee, S., Chen, J., Shi, RZ and Wang, S.M. (2004 ). SAGE is much more sensitive than EST for detecting low abundance transcripts. BMC Genomics, 5(1), 1-4. Tuteja, R. and Tuteja, N. (2004). Serial analysis of gene expression: applications in human studies. Journal of Biomedicine and Biotechnology, 2, 113-120. Yamamoto, M., Wakatsuki, T., Hada, A. and Ryo, A. (2001). Use of serial analysis of gene expression (SAGE) technology. Journal of Immunological Methods, 250, 45-66.