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The first complete genome sequence was published in 1977 (bacteriophage PHICHI174 DNA) and the first complete genome of a freeliving organism has become available in 1995 (Haemophilus influenza). Since then the velocity of producing new sequence data is rapidly increasing. Today more than 1,000 complete genomes are known, and thousands are on the way. The task is now to convert this information into as much biological knowledge as possible. Many tools for genome analysis, phylogeny, motif discovery, etc. have been developed, but still we do not fully understand important issues of molecular biology. How are DNAbinding proteins targeting and binding to DNA? How are nucleotide sequences folding? How are genomes organized and evolving or how is the gene expression regulated? These are only some of the still unsolved questions. One main reason for so many open issues is that genome analysis is currently almost exclusively done by treating the sequence as a character string. In this book a new approach combining different perspectives on nucleotide sequences is introduced. This allows recognizing sequence patterns that are hidden in the usual character string representation.
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