Results 41 to 50 of about 237,694 (293)

Grinder: a versatile amplicon and shotgun sequence simulator [PDF]

Nucleic Acids Research, 2012
We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists.
Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip, Tyson, Gene W.   +4 more
openaire   +3 more sources

Integrated DNA walking system to characterize a broad spectrum of GMOs in food/feed matrices [PDF]

, 2015
Background: In order to provide a system fully integrated with qPCR screening, usually used in GMO routine analysis, as well as being able to detect, characterize and identify a broad spectrum of GMOs in food/feed matrices, two bidirectional DNA walking ...
De Loose, Marc, Deforce, Dieter, Fraiture, Marie-Alice, Herman, Philippe, Lefèvre, Loic, Roosens, Nancy H, Taverniers, Isabel   +6 more
core   +6 more sources

Nanopore amplicon sequencing v2

, 2022
This protocol describes the step-by-step procedures for performing nanopore amplicon sequencing using the latest Kit 14 chemistry. The method is versatile and can be applied to a wide range of sequence-based analyses, including human microbiome profiling and biodiversity assessment using environmental DNA (eDNA metabarcoding).
openaire   +1 more source

Reproducibility and quantitation of amplicon sequencing-based detection [PDF]

The ISME Journal, 2011
Abstract To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined.
Jizhong, Zhou, Liyou, Wu, Ye, Deng, Xiaoyang, Zhi, Yi-Huei, Jiang, Qichao, Tu, Jianping, Xie, Joy D, Van Nostrand, Zhili, He, Yunfeng, Yang   +9 more
openaire   +2 more sources

PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing

BMC Bioinformatics, 2020
Background The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing.
Alexis Robitaille, Rosario N. Brancaccio, Sankhadeep Dutta, Dana E. Rollison, Marcis Leja, Nicole Fischer, Adam Grundhoff, Tarik Gheit, Massimo Tommasino, Magali Olivier   +9 more
doaj   +1 more source

High-Resolution Analysis of the Efficiency, Heritability, and Editing Outcomes of CRISPR/Cas9-Induced Modifications of NCED4 in Lettuce (Lactuca sativa). [PDF]

, 2018
CRISPR/Cas9 is a transformative tool for making targeted genetic alterations. In plants, high mutation efficiencies have been reported in primary transformants. However, many of the mutations analyzed were somatic and therefore not heritable.
Bertier, Lien D, Bradford, Kent J, Britt, Anne B, Huo, Heqiang, Michelmore, Richard W, Ron, Mily   +5 more
core   +2 more sources

PCR amplicon next generation sequencing v3

, 2022
Preparation of Amplicons for deep sequencing is based on two PCR steps. The genomic loci of interest is enriched in a first PCR including a stubber sequence to both ends of the molecule. For the subsequent barcoding PCR the stubber sequence is targeted and the full NGS sequencing adapter including dual barcodes are introduced to the molecule ends ...
Susanne Kreutzer, Lilly van de Venn, Charles Yeh, Mark DeWitt   +3 more
openaire   +1 more source

Strategy for Modular Tagged High-Throughput Amplicon Sequencing [PDF]

Applied and Environmental Microbiology, 2011
ABSTRACT The use and validation of a strategy that allows a universal set of bar-coded sequencing primers to be appended to an amplified PCR product is described. The strategy allows a modular approach, in that the same bar code can be used with two or more target-specific primer sets, even simultaneously.
de Carcer, Daniel Aguirre, Denman, Stuart E., McSweeney, Chris, Morrison, Mark   +3 more
openaire   +4 more sources

Drug resistance outcomes of long-term ART with tenofovir disoproxil fumarate in the absence of virological monitoring [PDF]

, 2018
Objectives: The resistance profiles of patients receiving long-term ART in sub-Saharan Africa have been poorly described. This study obtained a sensitive assessment of the resistance patterns associated with long-term tenofovir-based ART in a ...
Appiah, Lambert T, Beloukas, Apostolos, Chadwick, David, Geretti, Anna Maria, Phillips, Richard O, Ruggiero, Alessandra, Sarfo, Fred S, Smith, Colette, Stockdale, Alexander J, Villa, Giovanni   +9 more
core   +3 more sources

Strategy for the identification of micro-organisms producing food and feed products : bacteria producing food enzymes as study case [PDF]

, 2020
Recent European regulations require safety assessments of food enzymes (FE) before their commercialization. FE are mainly produced by micro-organisms, whose viable strains nor associated DNA can be present in the final products.
De Keersmaecker, Sigrid C. J., Deckers, Marie, Deforce, Dieter, Denayer, Sarah, Fraiture, Marie-Alice, Heyndrickx, Marc, Roosens, Nancy H. C., Vanneste, Kevin, Winand, Raf   +8 more
core   +2 more sources