用于微生物鉴定微阵列的菌株/种特异性探针设计。
Strain/species-specific probe design for microbial identification microarrays.
机构信息
Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
出版信息
Appl Environ Microbiol. 2013 Aug;79(16):5085-8. doi: 10.1128/AEM.01124-13. Epub 2013 Jun 7.
Abstract
Specific identification of microorganisms in the environment is important but challenging, especially at the species/strain level. Here, we have developed a novel k-mer-based approach to select strain/species-specific probes for microbial identification with diagnostic microarrays. Application of this approach to human microbiome genomes showed that multiple (≥10 probes per strain) strain-specific 50-mer oligonucleotide probes could be designed for 2,012 of 3,421 bacterial strains of the human microbiome, and species-specific probes could be designed for most of the other strains. The method can also be used to select strain/species-specific probes for sequenced genomes in any environments, such as soil and water.
摘要
环境中微生物的特异性鉴定很重要，但具有挑战性，尤其是在种/菌株水平。在这里，我们开发了一种新的基于 k- -mer 的方法，用于通过诊断微阵列选择微生物鉴定的菌株/种特异性探针。该方法在人类微生物组基因组中的应用表明，可针对人类微生物组的 3421 种细菌菌株中的 2012 种设计多个（每个菌株≥10 个探针）菌株特异性 50- 碱基寡核苷酸探针，并且可为大多数其他菌株设计种特异性探针。该方法还可用于为任何环境（如土壤和水）中的测序基因组选择菌株/种特异性探针。
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