A web-based adaptive tutor to teach PCR primer design

2011 ◽  
Vol 40 (1) ◽  
pp. 8-13 ◽  
Author(s):  
Janneke R. van Seters ◽  
Joan Wellink ◽  
Johannes Tramper ◽  
Martin J. Goedhart ◽  
Miriam A. Ossevoort
Keyword(s):  
Primer Design ◽  
Web Based ◽  
Pcr Primer

scholarly journals The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jie Yuan ◽  
Ji Yi ◽  
Meixiao Zhan ◽  
Qingqing Xie ◽  
Ting Ting Zhen ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Secondary Structures ◽  
Primer Design ◽  
Design Tool ◽  
Web Based ◽  
Tumour Diagnosis ◽  
Design Software ◽  
Nonspecific Amplification ◽  
User Friendly ◽  
Pcr Primer

Abstract Background A large number of variants have been employed in various medical applications, such as providing medication instructions, disease susceptibility testing, paternity testing, and tumour diagnosis. A high multiplicity PCR will outperform other technologies because of its lower cost, reaction time and sample consumption. To conduct a multiplex PCR with higher than 100 plex multiplicity, primers need to be carefully designed to avoid the formation of secondary structures and nonspecific amplification between primers, templates and products. Thus, a user-friendly, highly automated and highly user-defined web-based multiplex PCR primer design software is needed to minimize the work of primer design and experimental verification. Results Ultiplex was developed as a free online multiplex primer design tool with a user-friendly web-based interface (http://ultiplex.igenebook.cn). To evaluate the performance of Ultiplex, 294 out of 295 (99.7%) target primers were successfully designed. A total of 275 targets produced qualified primers after primer filtration, and 271 of those targets were successfully clustered into one compatible PCR group and could be covered by 108 primers. The designed primer group stably detected the rs28934573(C > T) mutation at lower than a 0.25% mutation rate in a series of samples with different ratios of HCT-15 and HaCaT cell line DNA. Conclusion Ultiplex is a web-based multiplex PCR primer tool that has several functions, including batch design and compatibility checking for the exclusion of mutual secondary structures and mutual false alignments across the whole genome. It offers flexible arguments for users to define their own references, primer Tm values, product lengths, plex numbers and tag oligos. With its user-friendly reports and web-based interface, Ultiplex will provide assistance for biological applications and research involving genomic variants.

scholarly journals Degenerate PCR primer design for the specific identification of rhinovirus C

2015 ◽  
Vol 214 ◽  
pp. 15-24 ◽  
Author(s):  
Young Ran Nam ◽  
Uk Lee ◽  
Han Seok Choi ◽  
Kyoung Jin Lee ◽  
Nari Kim ◽  
...  
Keyword(s):  
Primer Design ◽  
Degenerate Pcr ◽  
Specific Identification ◽  
Rhinovirus C ◽  
Pcr Primer

scholarly journals VizPrimer: a web server for visualized PCR primer design based on known gene structure

2011 ◽  
Vol 27 (24) ◽  
pp. 3432-3434 ◽  
Author(s):  
Y. Zhou ◽  
W. Qu ◽  
Y. Lu ◽  
Y. Zhang ◽  
X. Wang ◽  
...  
Keyword(s):  
Gene Structure ◽  
Web Server ◽  
Primer Design ◽  
Pcr Primer

scholarly journals Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

2008 ◽  
Vol 9 (1) ◽  
Author(s):  
Kelvin Li ◽  
Anushka Brownley ◽  
Timothy B Stockwell ◽  
Karen Beeson ◽  
Tina C McIntosh ◽  
...  
Keyword(s):  
Computational Methods ◽  
Primer Design ◽  
Design Effectiveness ◽  
Pcr Primer

Primer Prim’r: A web based server for automated primer design

2004 ◽  
Vol 5 (1/2) ◽  
pp. 13-21 ◽  
Author(s):  
John K. Everett ◽  
Thomas B. Acton ◽  
Gaetano T. Montelione
Keyword(s):  
Primer Design ◽  
Web Based
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