Finding a match between collections establishes genome identity. Either or both of these collections might be incomplete or unordered, or might contain errors, including symbol insertions and symbol deletions. In DNA fingerprinting, for example, an unknown collection of DNA fragments, typically a few tens to thousands of bases long, is compared with one of several known collections of DNA fragments contained in a library. These bases are adenine (A), guanine (G),cytosine (C), and thymine (T). Graduating from SpellingДЄ DNA sequence is analogous to a sentence in English in which the letters correspond to four types of organic molecules,called bases. These tasks all rely, in large part, on comparing an unfamiliar DNA sequence to one that is already known,establishing islands of similarity, and then forming a hypothesis about the function or meaning of the new sequence. This question seems to be of both fundamental and timely importance now that DNA sequencing figures so heavily into such important endeavors as DNA fingerprinting, pathogen detection, gene finding, genealogy study, and evolutionary tree reconstruction. Should we attempt to deduce the biological function and the genetic family tree of an organism simply by comparing individual parts, or rather, should we set a more ambitious goal and try to guess the overall blueprint for the genomic construction? Danchin echoes this question by asking whether it is the individual components of a gene or the relationships among them that define a gene. The question asked whether a boat whose planks have all been replaced one by one over time is still the same boat.

One of the pioneers of microbial genomics, Antoine Danchin,recalls in his book Delphic Boat an ancient question originally posed to the oracle of Delphi.

Dna sequence