Shotgun optical maps of the whole Escherichia coli O157:H7 genome
Shotgun optical maps of the whole Escherichia coli O157:H7 genome
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DOI：
10.1101/gr.172101
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发表时间：
2001-09-01
期刊：
影响因子：
7
通讯作者：
Schwartz, DC
中科院分区：
文献类型：
--
作者：
Lim, A;Dimalanta, ET;Schwartz, DC
我们已经构建了Nhe1和Xho1光学地图大肠杆菌O157：H7仅从基因组DNA分子提供了一个独特的有价值的支架重叠群封闭和序列验证。E.大肠杆菌O157：H7是在受污染的食物和水中发现的常见病原体。我们的方法避免了对克隆、PCR产物和杂交分析的需要，因为图谱是由单个DNA分子的集合构建的。尽管测序技术取得了进步，但细菌基因组的鸟枪测序仍然是劳动密集型的。这部分是由于在精加工的最后阶段需要人工干预。机器视觉技术的进步提高了光学测绘对这一问题的适用性，提高了测绘吞吐量，并为测绘的完全自动化开辟了道路。比较了地图和序列数据，其特征在于序列的差距和指导新生的组件。
We have constructed Nhe1 and Xho1 optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.