标题:ARDEP, a Rapid Degenerate Primer Design Pipeline Based onk-mers for Amplicon Microbiome Studies
作者:Wu, Yueni; Feng, Kai; Wei, Ziyan; Wang, Zhujun; Deng, Ye
作者机构:[Wu, Yueni; Feng, Kai; Wang, Zhujun; Deng, Ye] Chinese Acad Sci, Res Ctr Ecoenvironm Sci, Key Lab Environm Biotechnol, Beijing 100085, Peoples R China 更多
通讯作者:Deng, Y(yedeng@rcees.ac.cn)
通讯作者地址:Deng, Y (corresponding author), Chinese Acad Sci, Res Ctr Ecoenvironm Sci, Key Lab Environm Biotechnol, Beijing 100085, Peoples R China.; Deng, Y (cor 更多
来源:INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
出版年:2020
卷:17
期:16
页码:1-12
DOI:10.3390/ijerph17165958
关键词:bioinformatic program; primer design; k-mer; analysis platform; primer; assessment
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.
收录类别:SCOPUS;SCIE;SSCI
资源类型:期刊论文
原文链接:https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089701326&doi=10.3390%2fijerph17165958&partnerID=40&md5=f9f7bbc326d4ca438b56ee64f519ccb8
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