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PrimerExplorer specifications

Information


Unique identifier OMICS_33525
Name PrimerExplorer
Interface Web user interface
Restrictions to use None
Input format TXT, FASTA, Genbank
Computer skills Basic
Version 5.0
Stability Stable
Requirements
Java Runtime Environment
Maintained Yes

PrimerExplorer citations

 (205)
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Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification

2018
PLoS One
PMCID: 5919678
PMID: 29698484
DOI: 10.1371/journal.pone.0196409
call_split See protocol

[…] Six primers were designed based on specific sequence (PtRA68) for early detection P. triticina using Primer Explorer V4 software (http://primerexplorer.jp/e). LAMP primers used in the study are listed in . The structure of the LAMP primers and their complementarity to target DNA used in the study are shown in . […]

library_books

Real time Detection and Monitoring of Loop Mediated Amplification (LAMP) Reaction Using Self quenching and De quenching Fluorogenic Probes

2018
Sci Rep
PMCID: 5883045
PMID: 29615801
DOI: 10.1038/s41598-018-23930-1

[…] probe. While no work-around is possible for a loop primer that does not contain the candidate T residue, this can be easily addressed while designing a LAMP primer set de novo. In our experience, the PrimerExplorer™ V4 software (Eiken Chemical Co., Ltd., Tokyo, Japan) invariably generates multiple sets of loop primers, allowing a greater flexibility in selecting loop primers which are candidate fo […]

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Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription Loop Mediated Isothermal Amplification

2018
Sci Rep
PMCID: 5830622
PMID: 29491389
DOI: 10.1038/s41598-018-22102-5
call_split See protocol

[…] gned using Primer Explorer v4 (Eiken), and blasted using Primer-BLAST (NCBI) against genomes of interest. Primers selection was prioritized as described in “A Guide to LAMP primer designing” (https://primerexplorer.jp/e/v4_manual/). In addition, primers were selected to not have four guanines in a row. A set of six olgionucleotides primers were used for the ZIKV RT-LAMP assay targeting the consens […]

library_books

Lateral Flow Loop Mediated Isothermal Amplification Test with Stem Primers: Detection of Cryptosporidium Species in Kenyan Children Presenting with Diarrhea

2018
PMCID: 5846371
PMID: 29681951
DOI: 10.1155/2018/7659730

[…] o design LAMP primers. Briefly, the forward and backward outer primers (F3/B3) and the forward and backward inner primers (FIP/BIP) were designed using the primer explorer version 3 software (https://primerexplorer.jp/e/). The loop forward and backward primers (LF/LB), stem forward and backward primers (SF/SB), and the probe were designed manually following published conditions [, ]. All the prime […]

library_books

Real time fluorescence loop mediated isothermal amplification assay for direct detection of egg drop syndrome virus

2018
PMCID: 5811957
PMID: 29439721
DOI: 10.1186/s12917-018-1364-9

[…] Six specific RealAmp primers (F3, B3, FIP, BIP, LF and LB) were designed using PrimerExplorer V5 software (Eiken Chemical Co. Ltd., Tokyo, Japan) based on the fiber gene sequence of the EDSV (GenBank accession No.Y09598.1). The genome positions of RealAmp primers in EDSV genome […]

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Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop Mediated Isothermal Amplification (TEC LAMP) Assay for the Detection of Bacterial Meningitis Pathogens

2018
Int J Mol Sci
PMCID: 5855746
PMID: 29425124
DOI: 10.3390/ijms19020524
call_split See protocol

[…] d the IAC template was a 500 bp random DNA gBlocks® Gene Fragment () purchased from Integrated DNA Technologies (Leuven, Belgium). These targets were used to design TEC-LAMP oligonucleotides () using PrimerExplorer V4 (Eiken Chemical, Tokyo, Japan). Standard desalted oligonucleotide primers were synthesized by Integrated DNA Technologies. TEC primer/probes for S. pneumoniae, N. meningitidis, H. in […]

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