The development of high-throughput sequencing technologies that parallelize the sequencing process by making it possible to produce millions of sequences at once (i.e., in parallel) has made sequence-based expression analysis increasingly popular. Since the first publication on using massively parallel signature sequencing (i.e., one particular method of high-throughput sequencing, among many) in gene expression analysis in 2000 (Brenner, et al., 2000), different manufacturers have developed various technologies for such sequencing (Ansorge, 2009). They are all based on common principles of massively parallel shotgun sequencing (a method used for sequencing long DNA strands named by analogy with the quasi-random rapidly-expanding firing pattern of a shotgun) of cDNA (complimentary DNA) libraries derived from total RNA or special RNAs depending on the objective of the study. Each of the cDNA fragments is flanked on one (single-end sequencing) or both (paired-end sequencing) ends by special oligonucleotides or adapters to be attached to the surface of the appropriate sequencing platform. Then clonal amplification produces ~1,000 copies of a single member of the template library (i.e., copies, produced from a specific cDNA fragment); this set of
