ARDEP, a Rapid Degenerate Primer Design Pipeline Based onk-mers for Amplicon Microbiome Studies
文献类型：期刊论文
| 作者 | Wu, Yueni; Feng, Kai ; Wei, Ziyan; Wang, Zhujun; Deng, Ye
|
| 刊名 | INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
 |
| 出版日期 | 2020-08 |
| 卷号 | 17期号:16页码:1-9 |
| 关键词 | bioinformatic program primer design k-mer analysis platform primer assessment |
| 英文摘要 | The survey of microbial diversity in various environments has relied upon the widespread use of well-evaluated amplification primers for taxonomic marker genes (e.g., prokaryotic 16S and fungal ITS). However, it is urgent to develop a fast and accurate bioinformatic program to design primers for microbial functional genes to explore more mechanisms in the microbial community. Here, we provide a rapid degenerate primer design pipeline (ARDEP) based on thek-mer algorithm, which can bypass the time-consuming step of sequence alignment to greatly reduce run times while ensuring accuracy. In addition, we developed an open-access platform for the implementation of primer design projects that could also calculate the amplification product length, GC content, Annealing Temperature (Tm), and Delta G of primer self-folding, and identify covered species and functional groups. Using this new platform, we designed primers for several functional genes in the nitrogen cycle, includingnapAandamoA. Our newly designed primers achieved higher coverage than the commonly used primers for all tested genes. The program and the associated platform that applied thek-mer algorithm could greatly enhance the design and evaluation of primers for environmental microbiome studies. |
| 源URL | [http://ir.rcees.ac.cn/handle/311016/45136]  |
| 专题 | 生态环境研究中心_中国科学院环境生物技术重点实验室 |
| 推荐引用方式 GB/T 7714 | Wu, Yueni,Feng, Kai,Wei, Ziyan,et al. ARDEP, a Rapid Degenerate Primer Design Pipeline Based onk-mers for Amplicon Microbiome Studies[J]. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH,2020,17(16):1-9. |
| APA | Wu, Yueni,Feng, Kai,Wei, Ziyan,Wang, Zhujun,&Deng, Ye.(2020).ARDEP, a Rapid Degenerate Primer Design Pipeline Based onk-mers for Amplicon Microbiome Studies.INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH,17(16),1-9. |
| MLA | Wu, Yueni,et al."ARDEP, a Rapid Degenerate Primer Design Pipeline Based onk-mers for Amplicon Microbiome Studies".INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 17.16(2020):1-9. |
入库方式： OAI收割
来源：生态环境研究中心
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