Bellingham Research Institute, Bellingham, Washington, USA.
Genome Biol Evol. 2013;5(6):1176-84. doi: 10.1093/gbe/evt085.
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.
光学作图是一种产生细菌或真核染色体有序限制图谱的技术。我们开发了一种新方法，BOP 方法，用于比较完整基因组的实验光学图谱和计算机光学图谱，以推断每个基因组中短 DNA 序列（bops）的存在/缺失。BOP 方法，由四个程序的光学作图套件实现，避免了全基因组多重比对的必要性，并允许基于光学图谱进行可靠的菌株分型和聚类。我们已经将光学作图套件应用于 125 株不动杆菌属，包括 11 个完全测序的基因组和来自美国三家军事医院的 114 个不动杆菌复合体。我们发现光学作图完全解决了所有 125 个菌株。信号噪声分析表明，当将 125 个菌株一起考虑时，几乎有 1/3 的实验片段被错误识别。我们发现，这 125 个基因组可以分为三个聚类，其中两个聚类包含已测序的基因组。聚类后的信号噪声分析表明，只有 3.5%的实验限制片段被错误识别。还展示了包含已测序基因组的两个聚类的最小生成树。我们开发的程序为分析光学图谱数据提供了比以前更严格的方法。
