scholarly journals MDC-Analyzer: A novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites

BioTechniques ◽  
2014 ◽  
Vol 56 (6) ◽  
Author(s):  
Lixia Tang ◽  
Xiong Wang ◽  
Beibei Ru ◽  
Hengfei Sun ◽  
Jian Huang ◽  
...  
Keyword(s):  
Primer Design ◽  
Design Tool ◽  
Degenerate Primer

scholarly journals URPD: a specific product primer design tool

2012 ◽  
Vol 5 (1) ◽  
pp. 306 ◽  
Author(s):  
Li-Yeh Chuang ◽  
Yu-Huei Cheng ◽  
Cheng-Hong Yang
Keyword(s):  
Primer Design ◽  
Design Tool ◽  
Specific Product

scholarly journals Accumulating Variation at Conserved Sites in Potyvirus Genomes Is Driven by Species Discovery and Affects Degenerate Primer Design

PLoS ONE ◽  
2008 ◽  
Vol 3 (2) ◽  
pp. e1586 ◽  
Author(s):  
Linda Zheng ◽  
Paul J. Wayper ◽  
Adrian J. Gibbs ◽  
Mathieu Fourment ◽  
Brendan C. Rodoni ◽  
...  
Keyword(s):  
Primer Design ◽  
Degenerate Primer ◽  
Species Discovery

scholarly journals MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics

2016 ◽  
Vol 8 (1) ◽  
Author(s):  
Ram Vinay Pandey ◽  
Walter Pulverer ◽  
Rainer Kallmeyer ◽  
Gabriel Beikircher ◽  
Stephan Pabinger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Throughput ◽  
Primer Design ◽  
Design Tool ◽  
Methylation Analysis ◽  
Assay Design ◽  
Dna Methylation Analysis

HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis

2016 ◽  
Vol 23 (1) ◽  
pp. 27-29 ◽  
Author(s):  
Cesar M. Camilo ◽  
Gustavo M.A. Lima ◽  
Fernando V. Maluf ◽  
Rafael V.C. Guido ◽  
Igor Polikarpov
Keyword(s):  
Gene Cloning ◽  
High Throughput ◽  
Primer Design ◽  
Design Tool ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis

Degenerate Primer Design for Highly Variable Genomes

2015 ◽  
pp. 103-115 ◽  
Author(s):  
Kelvin Li ◽  
Susmita Shrivastava ◽  
Timothy B. Stockwell
Keyword(s):  
Primer Design ◽  
Degenerate Primer

scholarly journals ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies

2020 ◽  
Vol 17 (16) ◽  
pp. 5958
Author(s):  
Yueni Wu ◽  
Kai Feng ◽  
Ziyan Wei ◽  
Zhujun Wang ◽  
Ye Deng
Keyword(s):  
Annealing Temperature ◽  
Gc Content ◽  
Primer Design ◽  
Degenerate Primer ◽  
Functional Genes ◽  
Marker Genes ◽  
Amplification Product ◽  
Design Projects ◽  
Taxonomic Marker ◽  
Fungal Its

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 the k-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 ΔG 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, including napA and amoA. Our newly designed primers achieved higher coverage than the commonly used primers for all tested genes. The program and the associated platform that applied the k-mer algorithm could greatly enhance the design and evaluation of primers for environmental microbiome studies.

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