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This book is a guide for users of new technologies, as it includes accurately proven protocols, allowing readers to prepare their samples for experiments. Additionally, it is a guide for the bioinformatics tools that are available for the analysis of the obtained tags, including the design of the software, the sources and the Web. Finally, the book provides examples of the application of these technologies to identify promoters, annotate genomes, identify new RNAs and reconstruct models of transcriptional control. Although examples mainly concern mammalians, the discussion expands to other groups of eukaryotes, where these approaches are complementing genome sequencing.