The complete sequencing of the human genome and several other genomes for model organisms and other scientifically or technologically important species has opened what has been dubbed the post-genomic era. Notwithstanding the continuing and fruitful sequencing projects, this phase has been marked by a strong emphasis on genome function. The promise that the sequence, once revealed, would pave the way to understanding a variety of other aspects of biology has not been fully realized. For instance, the effort to experimentally characterize the structure of proteins is more vigorous then ever and conformation prediction from sequence information alone, despite progress, remains a challenge. Even coming up with a complete gene list for a newly sequenced genome is still a challenge and there is evidence that the transcribed fraction of the genome has been underestimated. Large collaborative efforts, such as the ENCODE project, have been launched to throw an array of experimental technologies at the problem of functional characterization of the genome - including but definitely not limited to more sequencing and in depth comparative genomics. One such technology is the tiling microarray (TM). A variation on the now widespread DNA microarray, the TM contains probes that correspond to regularly spaced position on a target genome, irrespective of their annotation as transcripts, promoters or any other functional determination. Therefore, they are made possible by genome sequencing efforts and complement them as high throughput technologies for the characterization of a variety of functional aspects of the genome. In combination with diverse assays, they have been applied to tasks such as transcript mapping and copy number variation and DNA replication analysis.
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