The term annotation is broadly used to define any special features of, or knowledge about, specific regions of sequence. Intense focus on automated gene finders has diluted the definition in many contexts to refer primarily to gene annotation, but it should be remembered that many non-gene features also qualify as annotation. Indeed, one could define annotation tracks on a pathogen genome for regions conserved across all strains/isolates, and further define those conserved regions that are apparently unique when compared to all other known sequence. Diagnostic and forensic signature regions derived from these conserved/unique annotation tracks could themselves form additional annotation tracks. Our discussion of annotation here will be heavily focused on aspects relevant to the design and selection of good detection and forensic diagnostics.

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