Resequencing is useful for relating phenotype to genotype and for analyzing natural variation. It has been used to study the acquisition of antibiotic resistance [1, 2] , the analysis of variation in pathogenic bacteria and viruses [3] [4] [5] [6] [7] , and to study the experimental evolution of bacteria and yeast [8] [9] [10] [11] . Methods of resequencing utilize micro-arrays [2, 7, 10] , polonies [9] or sequencing-by-synthesis technology [12] . The Comparative Genome Sequencing service provided by Nimblegen Systems Inc. is a hybridization-based method and consists of two steps [2] . In the first step, an experimental and reference genomic DNA sample are labeled and hybridized to microarrays containing ~30-mer 'tiled' oligonucleotides spaced every ~7 bp of the genome on both strands. Probes cover every nucleotide of the genome and are designed to have isothermal hybridization characteristics. Probes showing differences in signal intensity are flagged as Regions Of Interest (ROIs) for further investigation. A second microarray is then designed to interrogate the ROIs at single base-pair resolution, with all four possible nucleotides synthesized for each interrogated position on both strands (8 probes per position). If the sequence difference is a single-base polymorphism, the pattern of probe intensities at that position will be discernibly different than expected. Other types of sequence differences such as insertions/deletions (indels) or differences of more than one bp will not be determined conclusively.