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PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight
2011 Computer applications in the biosciences : CABIOS  
Motivation: PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing  ...  Results: PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data  ...  No existing tools specifically address the issues associated with designing barcoded polymerase chain reaction (PCR) primers for community analysis.  ... 
doi:10.1093/bioinformatics/btr087 pmid:21349862 pmcid:PMC3072552 fatcat:5hjzj2h6wfccxanexj2mkyksse

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

Kirsten A. Ziesemer, Allison E. Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-García, Mark Aldenderfer, Camilla Speller (+8 others)
2015 Scientific Reports  
and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing.  ...  Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent  ...  22 , in which a targeted variable region of the 16S rRNA gene is amplified by polymerase chain reaction (PCR), deep sequenced using Next Generation Sequencing (NGS) technology, and compared to a reference  ... 
doi:10.1038/srep16498 pmid:26563586 pmcid:PMC4643231 fatcat:mkvdrkublbh2rgg6bualvt6tsi

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

Rui M Ferreira, Joana Pereira-Marques, Ines Pinto-Ribeiro, Jose L Costa, Fatima Carneiro, Jose C Machado, Ceu Figueiredo
2017 Gut  
taxonomic analysis of barcoded polymerase chain reaction primers.  ...  PrimerProspector: de novo design and funds through Fundação para a Ciência e a Tecnologia (FCT)/Ministério da Ciência,  ... 
doi:10.1136/gutjnl-2017-314205 pmid:29102920 pmcid:PMC5868293 fatcat:dpbq4ykx25gkpfmj37pv3gamqy

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

Luisa W. Hugerth, Anders F. Andersson
2017 Frontiers in Microbiology  
for handling these data, from sample collection and library preparation to statistical analysis.  ...  However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training.  ...  By flanking the region of interest with two primers, its copy number is doubled at every polymerization cycle, hence the term "polymerase chain reaction".  ... 
doi:10.3389/fmicb.2017.01561 pmid:28928718 pmcid:PMC5591341 fatcat:rxtwpsadbzbivfavm7cwqfvc34

Alpha diversity metrics for noisy OTUs [article]

Robert C. Edgar, Henrik Flyvbjerg
2018 biorxiv/medrxiv   pre-print
The in-sample (alpha) diversity of Operational Taxonomic Units (OTUs) is often summarized by metrics such as richness or entropy which are calculated from observed abundances, or by estimators such as  ...  However, errors introduced by next-generation amplicon sequencing tend to induce spurious OTUs and spurious counts in OTU tables, both of which are especially prevalent at low abundances.  ...  11 practice, and we therefore believe that it is generally not possible to make reliable estimates of the full diversity of a sample from observed microbial OTUs.  ... 
doi:10.1101/434977 fatcat:zieyuqe6tzh35hu5scqrshcakq

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

Kirsten A Ziesemer, Allison E Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T Ozga, Bernd W Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C Salazar-García, Mark Aldenderfer, Camilla Speller (+10 others)
2018
and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing.  ...  Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent  ...  22 , in which a targeted variable region of the 16S rRNA gene is amplified by polymerase chain reaction (PCR), deep sequenced using Next Generation Sequencing (NGS) technology, and compared to a reference  ... 
doi:10.17863/cam.33198 fatcat:5zhrya65inhbxfzbnltslakwsa

Optimising and applying RNA based approaches to identify active nitrifiers in coastal sediments

Fabien Cholet
2021
Then, the effect of the RT protocol itself on RT-Q-PCR and RT-PCR- sequencing results will be evaluated by testing a combination of four different RT enzymes and two priming strategie [...]  ...  Since the beginning of the industrial revolution, nitrogen has become a major pollutant of marine and coastal ecosystems due to the huge rise in the use of inorganic fertiliser.  ...  The PrimerProspector search returned four and two possible regions for the design of the forward and reverse primers respectively.  ... 
doi:10.5525/gla.thesis.82100 fatcat:xqtutvvw2nbo3jqoqpllotzm2a