Degenerate primer design via clustering

2004 ◽  
Author(s):  
X. Wei ◽  
D.N. Kuhn ◽  
Giri Narasimhan
Keyword(s):  
Primer Design ◽  
Degenerate Primer

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 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

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.

scholarly journals The degenerate primer design problem

2002 ◽  
Vol 18 (Suppl 1) ◽  
pp. S172-S181 ◽  
Author(s):  
C. Linhart ◽  
R. Shamir
Keyword(s):  
Design Problem ◽  
Primer Design ◽  
Degenerate Primer

scholarly journals DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies

2014 ◽  
Vol 80 (16) ◽  
pp. 5116-5123 ◽  
Author(s):  
Luisa W. Hugerth ◽  
Hugo A. Wefer ◽  
Sverker Lundin ◽  
Hedvig E. Jakobsson ◽  
Mathilda Lindberg ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Pcr Primers ◽  
Primer Design ◽  
Taxonomic Composition ◽  
Degenerate Primer ◽  
Rrna Gene ◽  
Multiple Sequence ◽  
High Coverage ◽  
Shotgun Metagenomics ◽  
Taxonomic Range

ABSTRACTThe taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571–1579, 2011,http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.

scholarly journals In silico design and validation of a highly degenerate primer pair: a systematic approach

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Prosper Obed Chukwuemeka ◽  
Haruna Isiyaku Umar ◽  
Oluwatoyin Folake Olukunle ◽  
Oluwaseyi Matthew Oretade ◽  
Christopher Busayo Olowosoke ◽  
...  
Keyword(s):  
In Silico ◽  
Biological Activities ◽  
Positive Control ◽  
Primer Design ◽  
Extensive Study ◽  
Degenerate Primer ◽  
Degenerate Primers ◽  
Software Program ◽  
Optimal Efficiency ◽  
Enzymatic Degradability

Abstract Background The techniques of amplifying genetic materials have enabled the extensive study of several biological activities outside the biological milieu of living systems. More recently, this approach has been extended to amplify population of genes, from evolutionarily related gene family for detection and evaluation of microbial consortial with several unique potentialities (e.g., enzymatic degradability). Conceivably, primer mixtures containing substitutions of different bases at specific sites (degenerate primers) have enabled the amplification of these genes in PCR reaction. However, the degenerate primer design problem (DPD) is a constraint to designing this kind of primer. To date, different algorithms now exist to solve various versions of DPD problem, many of which, only few addresses and satisfy the criteria to design primers that can extensively cover high through-put sequences while striking the balance between specificity and efficiency. The highly degenerate primer (HYDEN) design software program primarily addresses this variant of DPD problem termed “maximum coverage-degenerate primer design (MC-DPD)” and its heuristics have been substantiated for optimal efficiency from significant successes in PCR. In spite of the premium presented for designing degenerate primers, literature search has indicated relatively little use of its heuristics. This has been thought to result from the complexity of the program since it is run only by command-line, hence limiting its accessibility. To solve this problem, researchers have optionally considered the manual design of degenerate primers or design through software programs that provides accessibility through a graphical user interface (GUI). Realizing this, we have attempted in this study to provide a user-friendly approach for researchers with little or no background in bioinformatics to design degenerate primers using HYDEN Results Virtual Tests of our designed degenerate primer pair through in silico PCR substantiated the correspondence between efficiency and coverage with the target sequences as pre-defined by the initial HYDEN output, thereby validating the potentials of HYDEN to effectively solve the MC-DPD problem. Additionally, the designed primer-pair mechanistically amplified all sequences used as a positive control with no amplification observed in the negative controls. Conclusion In this study, we provided a turnkey protocol to simplify the design of degenerate primers using the heuristics of the HYDEN software program.

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