Abstract

A Ruler Array measures the distance between a set of microarray probes and a set of ex-perimentally defined locations in a nucleic acid, offering new possibilities for locating and characterizing changes in the nucleic acid sequence. Despite the known relevance of genomic changes to pathogens, cancer, development, and evolution, many of these changes evade detection by existing high-throughput techniques. Since a microarray can interrogate thou-sands or millions of probes at once, Ruler Arrays can screen a small genome or part of a mammalian sized genome for insertions, deletions, and inversions in a single experiment.