There are basic methodological requirements for any analysis of transcript structures and their differential distribution. The method should be able to measure the absolute and relative content of transcripts of a single gene and the abundance of transcripts of a large set of genes with different expression levels simultaneously. The most frequently used method of studying whole genome expression is DNA microarrays. This technique is based on measuring differential gene expression using two-color fluorescent hybridization of target fragments with specific DNA probes attached to the solid surface of a biochip. In different microarray platforms, such as Applied Biosystems, Affymetrix, Agilent, Illumina and others, oligonucleotides that are 25-70 bases in length representing specific gene coding regions are usually used as hybridization probes. Yet, there are serious limitations in using microarray technologies for transcriptome analysis (Irizarry, et al., 2005; Kawasaki, 2006). First, microarrays measure only the relative quantities of transcripts. Specifically, this technology suffers from fluorescence background and cross-hybridization problems that might lead to underestimating low-abundance transcripts or the expression levels of infrequently expressed genes. Second, the technique measures the activity of
