Cargando…

Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

BACKGROUND: Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the ampl...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sambo, Francesco, Finotello, Francesca, Lavezzo, Enrico, Baruzzo, Giacomo, Masi, Giulia, Peta, Elektra, Falda, Marco, Toppo, Stefano, Barzon, Luisa, Di Camillo, Barbara
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2018
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162885/ https://www.ncbi.nlm.nih.gov/pubmed/30268091 http://dx.doi.org/10.1186/s12859-018-2360-6

Ejemplares similares

Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak
por: Lavezzo, Enrico, et al.
Publicado: (2013)

Role of the Extracytoplasmic Function Sigma Factor SigE in the Stringent Response of Mycobacterium tuberculosis
por: Baruzzo, Giacomo, et al.
Publicado: (2023)

KDM2B in papillomavirus-related cancer
por: Peta, Elektra, et al.
Publicado: (2018)

Reducing bias in RNA sequencing data: a novel approach to compute counts
por: Finotello, Francesca, et al.
Publicado: (2014)

metaSPARSim: a 16S rRNA gene sequencing count data simulator
por: Patuzzi, Ilaria, et al.
Publicado: (2019)

Applications of Next-Generation Sequencing Technologies to Diagnostic Virology
por: Barzon, Luisa, et al.
Publicado: (2011)

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region
por: Lavezzo, Enrico, et al.
Publicado: (2016)

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms
por: Falda, Marco, et al.
Publicado: (2012)

Tuberculosis-Associated MicroRNAs: From Pathogenesis to Disease Biomarkers
por: Sinigaglia, Alessandro, et al.
Publicado: (2020)

PCR primers for an aldolase-B intron in acanthopterygian fishes
por: Quattro, Joseph M, et al.
Publicado: (2001)

Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results
por: Baruzzo, Giacomo, et al.
Publicado: (2022)

Eliciting the Functional Taxonomy from protein annotations and taxa
por: Falda, Marco, et al.
Publicado: (2016)

PCR and real-time PCR primers developed for detection and identification of Bifidobacterium thermophilum in faeces
por: Mathys, Sophie, et al.
Publicado: (2008)

A plastome primer set for comprehensive quantitative real time RT-PCR analysis of Zea mays: a starter primer set for other Poaceae species
por: Sharpe, Richard M, et al.
Publicado: (2008)

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing
por: Li, Kelvin, et al.
Publicado: (2012)

An improved allele-specific PCR primer design method for SNP marker analysis and its application
por: Liu, Jing, et al.
Publicado: (2012)

Universal probe-based intermediate primer-triggered qPCR (UPIP-qPCR) for SNP genotyping
por: Li, Baowei, et al.
Publicado: (2021)

Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers
por: Balcells, Ingrid, et al.
Publicado: (2011)

Assessing alternative base substitutions at primer CpG sites to optimise unbiased PCR amplification of methylated sequences
por: Candiloro, Ida L. M., et al.
Publicado: (2017)

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms
por: Bianco, Luca, et al.
Publicado: (2017)

Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping
por: Nakitandwe, Joy, et al.
Publicado: (2007)

PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences
por: Machida, Ryuji J., et al.
Publicado: (2012)

Reprogramming Methods Do Not Affect Gene Expression Profile of Human Induced Pluripotent Stem Cells
por: Trevisan, Marta, et al.
Publicado: (2017)

Design of an improved set of oligonucleotide primers for genotyping MeCP2(tm1.1Bird )KO mice by PCR
por: Miralvès, Julie, et al.
Publicado: (2007)

Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts
por: Martin, Kendall J, et al.
Publicado: (2005)

RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers
por: Dobosy, Joseph R, et al.
Publicado: (2011)

Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs
por: Vestheim, Hege, et al.
Publicado: (2008)

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
por: Klindworth, Anna, et al.
Publicado: (2013)

PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences
por: Machida, Ryuji J., et al.
Publicado: (2012)

SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation
por: da Maia, Luciano Carlos, et al.
Publicado: (2008)

Genome Sequencing of West Nile Virus from Human Cases in Greece, 2012
por: Barzon, Luisa, et al.
Publicado: (2013)

Single-tube multiplex PCR using type-specific E6/E7 primers and capillary electrophoresis genotypes 21 human papillomaviruses in neoplasia
por: Dictor, Michael, et al.
Publicado: (2011)

Fusion primer and nested integrated PCR (FPNI-PCR): a new high-efficiency strategy for rapid chromosome walking or flanking sequence cloning
por: Wang, Zhen, et al.
Publicado: (2011)

Curriculum development: a how to primer
por: Schneiderhan, Jill, et al.
Publicado: (2019)

IMP PCR primers detect single nucleotide polymorphisms for Anopheles gambiae species identification, Mopti and Savanna rDNA types, and resistance to dieldrin in Anopheles arabiensis
por: Wilkins, Elien E, et al.
Publicado: (2006)

Development of a highly sensitive real-time one step RT-PCR combined complementary locked primer technology and conjugated minor groove binder probe
por: Hong, JiYoung, et al.
Publicado: (2011)

Correction: PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences
por: Machida, Ryuji J., et al.
Publicado: (2015)

Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens
por: Nguyen, Anh To, et al.
Publicado: (2016)

Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers
por: Zhang, Qingrun, et al.
Publicado: (2007)

Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies
por: Wang, Yong, et al.
Publicado: (2009)

Cannot write session to /tmp/vufind_sessions/sess_akisp84qnkr2g81rvgb1klt19t