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Optical mapping is a technique that produces an ordered restriction map of a bacterial or eukaryotic chromosome. We have developed a new method, the BOP method, to compare experimental optical maps with in silico optical maps of complete genomes to infer the presence/absence of short DNA sequences (bops) in each genome. The BOP method, as implemented by the Optical Mapping suite of four programs, circumvents the necessity of whole-genome multiple alignments and permits reliable strain typing and clustering on the basis of optical maps. We have applied the Optical Mapping Suite to 125 strains of Acinetobacter sp., including 11 completely sequenced genomes and 114 Acinetobacter complex from three US military hospitals. We found that optical mapping completely resolves all 125 strains. Signal to noise analysis showed that when the 125 strains were considered together almost 1/3 of the experimental fragments were misidentified. We found that the set of 125 genomes could be divided into three clusters, two of which included sequenced genomes. Signal to noise analysis after clustering showed that only 3.5% of the experimental restriction fragments were misidentified. Minimum spanning trees of the two clusters that included sequenced genomes are presented. The programs we have developed provide a more rigorous approach for analyzing optical map data than previously existed.

Clustering Acinetobacter Strains by Optical Mapping