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Primer3 specifications

Information


Unique identifier OMICS_02325
Name Primer3
Alternative names Primer3Plus, Primer3-web, Primer3web, Primer_core
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Additional information


http://primer3plus.com/cgi-bin/dev/primer3plus.cgi http://primer3plus.com/primer3web/primer3web_input.htm

Information


Unique identifier OMICS_02325
Name Primer3
Alternative names Primer3Plus, Primer3-web, Primer3web, Primer_core
Interface Web user interface
Restrictions to use None
Programming languages C, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Additional information


http://primer3plus.com/cgi-bin/dev/primer3plus.cgi http://primer3plus.com/primer3web/primer3web_input.htm

Publications for Primer3

Primer3 citations

 (8513)
call_split

Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription qPCR data in mice

2018
Sci Rep
PMCID: 5955877
PMID: 29769563
DOI: 10.1038/s41598-018-25389-6
call_split See protocol

[…] t subjected to reverse transcriptase PCR was used as control to assess gDNA contamination. Subsequently, RT-qPCR was carried out as described previously. Primer sequences (Table ) were designed using Primer3 software (http://bioinfo.ut.ee/primer3-0.4.0/) and amplification efficiencies were tested using a standard dilution series (6 points, dilution factor ¼, maximum input 10 µg) made from RT-qPCR […]

library_books

Semaphorin3A Signaling Is Dispensable for Motor Axon Reinnervation of the Adult Neuromuscular Junction

2018
eNeuro
PMCID: 5955010
PMID: 29774231
DOI: 10.1523/ENEURO.0155-17.2018

[…] ast Real-Time PCR System (Applied Biosystems) with the appropriate primer set () and FastStart Universal SYBR Green Master Mix (Roche). Primer sequences were obtained through the Harvard Primer bank, Primer3, or from previously published literature (; ). B2M was used as an internal control for all dCT calculations, and gene expression was calculated relative to the control condition. […]

library_books

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

2018
Hereditas
PMCID: 5952850
PMID: 29785177
DOI: 10.1186/s41065-018-0060-x

[…] the MISA software (http://pgrc.ipk-gatersleben.de/misa) with the parameters (unit size-min repeats) as follows: 1–12, 2–6, 3–5, 4–5, 5–4, 6–4. Primer pairs of each detected SSR locus were designed by Primer3 (http://bioinfo.ut.ee/primer3) with default parameters. A total of 210 primer pairs (Additional file ) were randomly chosen and synthesized for the validation of SSR markers. […]

library_books

Effects of cold acclimation and dsRNA injections on Gs1l gene splicing in Drosophila montana

2018
Sci Rep
PMCID: 5953924
PMID: 29765071
DOI: 10.1038/s41598-018-25872-0

[…] All primers for qPCR were designed based on D. montana genomic sequences using Primer3 (primer3.ut.ee) and NetPrimer (www.premierbiosoft.com/netprimer) programs (for primer sequences see Supplementary Table ). qPCR mix contained 10 µl of 2× Power SYBR Green PCR Master Mix (Bio-R […]

library_books

Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea

2018
Sci Rep
PMCID: 5943259
PMID: 29743510
DOI: 10.1038/s41598-018-25434-4

[…] .nlm.nih.gov/) and primers were designed using Primer BLAST (www.ncbi.nlm.nih.gov/tools/primer-blast) to PCR amplify gene fragments ranging between 200 and 450 bp in length and quality assessed using Primer3 (http://bioinfo.ut.ee/primer3/). Primer sets were designed to limit regions of homology (>20 bases) to other Eukaryotes by searching BLASTN (http://blast.ncbi.nlm.nih.gov/Blast) RefSeq accessi […]

library_books

Transcriptomic integration of D4R and MOR signaling in the rat caudate putamen

2018
Sci Rep
PMCID: 5943359
PMID: 29743514
DOI: 10.1038/s41598-018-25604-4

[…] and a sample from the frontal cortex of one pool of vehicle-injected animals were analysed. Based on rat D4R mRNA sequence (NM_012944.2), a set of primers was designed using the free online software Primer3 (http://primer3.sourceforge.net/) so intron-exon boundaries would not be crossed: (1) F 5′-TGCAGAAATTCAAGCCGTGG-3′ and R 5′-GCCAGGCTCACGATGAAGTA-3′. After reverse transcription, the PCR was pe […]

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Primer3 institution(s)
Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany

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