Anton van Leeuwenhoek, the microscopist, was in great demand as a party guest in fashionable Delft homes in the 17th century. He could be counted upon to bring along several hand-held microscopes with glass bead lenses on which he would mount diverse specimens, including scrapings from between the teeth of his fellow guests. Often we simply do not see what we do not (yet) understand. The problem in sequence analysis is compounded by the sheer quantity of the unanalyzed information and the indirect methods by which that information is deciphered. How much information is slipping through our current methods of classification and decoding, because we do not yet have the context by which to design the right search tools? Industrial labs, academic labs, granting agencies, and editors of journals often have clear visions and definitive opinions of what sorts of sequences are worth collecting, analyzing, and using; traditionally, gene sequences have been featured high on their lists. Indeed the annotation of any new genome begins and often ends with a catalogue of which genes are present. Often the sequences between genes are ignored. When such intergenic sequences are analyzed, they do not become neatly classified and organized into pre-existing databases, designed with genes in mind. Meaningful information, which often reveals itself in well-organized datasets, may not be visible at all.
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