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Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

Jian Ye, George Coulouris, Irena Zaretskaya, Ioana Cutcutache, Steve Rozen, Thomas L Madden
2012 BMC Bioinformatics  
Results: We present a new software tool called Primer-BLAST to alleviate the difficulty in designing target-specific primers.  ...  Choosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR).  ...  Yan Raytselis, Eric Sayers, Greg Schuler, Tao Tao, as well as members of the C++ toolkit group at the NCBI, for their work that has made this tool possible.  ... 
doi:10.1186/1471-2105-13-134 pmid:22708584 pmcid:PMC3412702 fatcat:uebbx2ls6rg7bbf6do55ubd56y

Primer designing in Primer-BLAST

A. A. Kozyreva, A. M. Zlotina, A. S. Golovkin, O. V. Kalinina, A. A. Kostareva
2021 Translational Medicine  
This work is an update for a previously published tutorial and provides a step-by-step guide to find target DNA regions, primers designing, and performing primer quality control.  ...  The polymerase chain reaction (PCR) is widely used in different areas.  ...  (https://www.ncbi. nlm.nih.gov/tools/primer-blast/index.cgi?  ... 
doi:10.18705/2311-4495-2021-8-3-37-52 fatcat:cxkgj4jxnjd2pmrjc25qzqybpi

Multiplexed reverse transcription real-time polymerase chain reaction for simultaneous detection of Mayaro, Oropouche, and Oropouche-like viruses

Felipe Gomes Naveca, Valdinete Alves do Nascimento, Victor Costa de Souza, Bruno Tardelli Diniz Nunes, Daniela Sueli Guerreiro Rodrigues, Pedro Fernando da Costa Vasconcelos
2017 Memórias do Instituto Oswaldo Cruz  
real-time polymerase chain reaction (RT-qPCR).  ...  The specificity of the multiplex assay was evaluated by Primer-Blast analysis against the entire GenBank database, and further against a panel of 17 RNA arboviruses.  ...  ACKNOWLEDGEMENTS To the Program for Technological Development in Tools for Health (PDTIS FIOCRUZ), for use of its facilities, and specifically the ILMD real-time PCR platform.  ... 
doi:10.1590/0074-02760160062 pmid:28591313 pmcid:PMC5452489 fatcat:wvbi73hcubce3oolmfx55oc4ju

Evaluating the specificity of primers employed for PCR-based diagnostics of Leishmaniases using multiple alignment analysis

Jane Eyre GABRIEL
2013 Estudos de Biologia  
The purpose of this study was to assess the specificity of distinct primers used in the molecular diagnosis for Leishmania detection by using biological sequence search and alignment tools.  ...  These findings emphasize the importance of selecting suitable primers for diagnosis of molecular diseases by conducting previous screenings in order to infer their specificity and identity against target  ...  Polymerase chain reactions have been characterized as the most important tool for basic and applied research in molecular biology and diagnostic methods for diseases (Yang & Rothman, 2004; Cancrini &  ... 
doi:10.7213/estud.biol.35.085.ao01 fatcat:lb7uiegk5vhu7htjlb24aonocy

Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis

Ruslan Kalendar, David Lee, Alan H. Schulman
2011 Genomics  
The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory.  ...  , bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction.  ...  Acknowledgments Web tools are available free to academic institutions, provided that they are used for non-commercial research and education only.  ... 
doi:10.1016/j.ygeno.2011.04.009 pmid:21569836 fatcat:eu2zfu55y5ghzoo3gf5vzsnmmi

Primer Design Using Polymerase Chain Reaction for SNPs Analysis in SLC22A1 rs622342 Encoding OCT1 as Metformin Main Transporter

Rochmy Istikharah, Vitarani Dwi Ananda Ningrum, Maylinda Gemantari
2018 Journal of Pharmacy and Nutrition Science  
This study aimed to design primers and to obtain an optimum condition for polymerase chain reaction (PCR) process that can detect the genetic polymorphism of SLC22A1 rs622342.  ...  Primers were computationally designed in primer 3 webpage and analyzed with Primer BLAST and Oligo Analyzer.  ...  ACKNOWLEDGEMENT The authors wish to express their deepest gratitude to the Directorate of Research and Community Service of Universitas Islam Indonesia through AIPT program.  ... 
doi:10.6000/1927-5951.2018.08.02.4 fatcat:dn3i3waljnga3dmlhh32cr43ce

From primer design to validation of results - is it possible by using free software only? / De la proiectarea primerilor la validarea rezultatelor - este posibil utilizând doar programe gratuite?

Adrian Man, Claudia Bănescu, Minodora Dobreanu, Cornel Fraefel
2015 Romanian Journal of Laboratory Medicine  
Due to the importance of optimal primer design in PCR assays, we will focus on primer designing and checking software, but we also present other useful free tools that can help researchers in the molecular  ...  PCR RT-PCR -Reverse transcription polymerase chain reaction  ...  One of the best known free online tools for primer design is Primer3 developed by Howard Hughes Medical Institute or Primer-BLAST from National Institutes of Health.  ... 
doi:10.1515/rrlm-2015-0022 fatcat:dii3uz2qazdknl3nxpvb7c2z5m

Rapid detection of herpes simplex virus 2: a SYBR-Green-based real-time PCR assay

Modhusudon Shaha, Bithi Roy, Mohammad Ariful Islam
2021 F1000Research  
The primers specific for HSV2 were designed using the Primer-BLAST tool and 120 base pairs of the polymerase gene were amplified using real-time PCR with SYBR Green dye.  ...  The threshold cycle (Ct) value for HSV2 reactions by designed primers was found to be an average of 22.55 for a standard copy number of viral DNA that may denote the efficiency of the primers.  ...  In this case, developing a new real-time polymerase chain reaction (RT-PCR) method for HSV-2 diagnosis can facilitate HSV2 detection.  ... 
doi:10.12688/f1000research.53541.1 pmid:34900232 pmcid:PMC8634051 fatcat:vtzkt3g5pjgk5ozevcb3ebp7dq

Rapid molecular authentication of the medicinal plant Taraxacum mongolium from its adulterants by ribosomal DNA internal transcribed spacer (ITS)-primed polymerase chain reaction

J Chao, M Chen, H Chen, M Lin, W Chang, K Chen, M Lee, M Lee
2010 Planta Medica  
Using a set of designed PCR primers, a highly specific 223 bp PCR product of T. formosanum was successfully amplified by PCR.  ...  This indicates that, our allele specific primers have high specificity and can accurately discriminate T. formosanum from its adulterant plants.  ...  Abbreviations PCR, Polymerase chain reaction; ITS, internal transcribed spacer; HPLC, high pressure liquid chromatography; RAPD, random amplified polymorphic DNA; PCR-RFLP, polymerase chain reaction-restriction  ... 
doi:10.1055/s-0030-1264309 fatcat:blzooiphwzg6jcrjkjdtabsb7m

Designing Polymerase Chain Reaction Primers Using Primer3Plus

Jui-Hung Hung, Zhiping Weng
2016 Cold Spring Harbor Protocols  
Some primer design tools will intentionally find primers targeting to junction sites to increase their specificity (Arvidsson et al. 2008 ).  ...  Many primer design tools are freely accessible on the Internet and some are specific to certain purposes (see Table 1 ).  ... 
doi:10.1101/pdb.prot093096 pmid:27574202 fatcat:xvhk32ajjvavvniz2um46kul54

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  
primers remains a challenging task.  ...  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  ...  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

IN SILICO OLIGONUCLEOTIDE PRIMER DESIGN FOR Campylobacter jejuni cytolethal distending toxin B GENE AMPLIFICATION

Rian Ka Praja
2021 Oceana Biomedicina Journal  
designed by using Primer-BLAST.  ...  It can be concluded that a primer set to amplify cdtB gene of C. jejunihas been successfully designed.However, a wet experiment is needed to run this primer set in the laboratory setting.  ...  Primer design Primer candidates for cdtB gene amplification were generated using the Primer-BLAST tool (https://www.ncbi.nlm.nih.gov/tools/primer-blast/).  ... 
doi:10.30649/obj.v4i1.88 fatcat:z54pbbxor5aifditbtngr6aqwe

Specific Primer for Human Bcl-2-Protein Expression Analysis

Dessy Nurul Jannah Patty, Tazkia Ayu Safitri, Henny Saraswati
2020 KnE Life Sciences  
Primer specificity was tested with Basic Local Alignment Tools (BLAST) tools and result in specific primer for human BCL-2 gene.  ...  This study aims to produce the Bcl-2 primer for qPCR method that specifically identifies the target gene, and can be used to see the BCL-2 gene expression level in cells.  ...  Conflict of Interest The authors declare that there are no conflicts of interest with respect to the research, authorship and/or publication of this article.  ... 
doi:10.18502/kls.v5i2.6438 fatcat:ha4vf5tsgfc47lpfj3zqagyfna

An improved single-round PCR leads to rapid and highly sensitive detection of Pneumocystis spp

Magali Chabé, Sara Khalife, Nausicaa Gantois, Gaël Even, Christophe Audebert
2014 Medical Mycology  
In order to standardize a polymerase chain reaction (PCR)-based method of Pneumocystis detection, we describe the development of an improved PCR method that targets the Pneumocystis mtLSUrRNA gene.  ...  Design of a new primer pair and PCR program with suitable parameters and optimization resulted in a simpler and faster single-round amplification assay.  ...  We thank Dr Isabelle Durand-Joly for providing the DNA extracts from human BALF and OW samples and Dr Laurence Delhaes for providing the pool of fungal DNA samples.  ... 
doi:10.1093/mmy/myu032 pmid:24965947 fatcat:okhdunoktba6phwnlxrryqimha

Design and in silico validation of polymerase chain reaction primers to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Maria Júlia P. Davi, Selma M. B. Jeronimo, João P. M. S. Lima, Daniel C. F. Lanza
2021 Scientific Reports  
AbstractAccurate designing of polymerase chain reaction (PCR) primers targeting conserved segments in viral genomes is desirable for preventing false-negative results and decreasing the need for standardization  ...  In this work, we designed and described a set of primers and probes targeting conserved regions identified from a multiple sequence alignment of 2341 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV  ...  The authors are also very grateful to the editors and the anonymous reviewers for the valuable comments and suggestions that helped improve the manuscript.  ... 
doi:10.1038/s41598-021-91817-9 pmid:34131209 pmcid:PMC8206341 fatcat:7b4a5jgjl5gyhivjqnckvg34ea
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