Abbey Darren A, Funt Jason, Lurie-Weinberger Mor N, Thompson Dawn A, Regev Aviv, Myers Chad L, Berman Judith
Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, Minneapolis, MN 55415 USA.
Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, MA 02142 USA.
Genome Med. 2014 Nov 20;6(11):100. doi: 10.1186/s13073-014-0100-8. eCollection 2014.
The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains of Candida albicans, the most prevalent human fungal pathogen. The YMAP pipeline (http://lovelace.cs.umn.edu/Ymap/) automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other pathogens with small genomes.
针对严重的真核病原体设计有效的抗菌疗法，需要清楚了解其高度可变的基因组。为便于分析这些病原体中的拷贝数变异、单核苷酸多态性和杂合性缺失事件，我们开发了一种流程，用于分析来自微阵列、深度测序以及限制性位点关联DNA序列实验的各种基因组规模数据集，这些数据集针对的是白色念珠菌（最常见的人类真菌病原体）的临床和实验室菌株。YMAP流程（http://lovelace.cs.umn.edu/Ymap/）能在一个直观的图中自动展示全基因组信息，并且很容易修改以用于分析其他小基因组病原体。
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