Primer3 protocols

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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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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 in pipelines

 (391)
2018
PMCID: 5794185
PMID: 29390041
DOI: 10.1371/journal.pone.0192343

[…] pairwise identities for the transcript and deduced amino acid sequences., the qrt-pcr primers for reference gene candidates, except for aftbp2, and also for the target gene afvp1, were designed with primer3: www primer tool [], using the following parameters: amplicon length around100 bp; primer size between 18 and 22 bp; melting temperature (tm) between 57 and 61°c; gc content between 40 […]

2018
PMCID: 5796704
PMID: 29394277
DOI: 10.1371/journal.pone.0192362

[…] expressed transcripts with functional annotation and high fold values were selected for validation through qrt-pcr. the fasta sequences of transcripts were retrieved and input in batch primer3 online tool by selecting the generic option and following criterion: product size of 100–200 (bp), primer size of 18–22 nts, melting temperature 59–62°c, rest of the parameters were default […]

2018
PMCID: 5800670
PMID: 29408927
DOI: 10.1371/journal.pone.0192253

[…] kobas software., to verify the accuracy and repeatability of the transcription sequencing results, 10 differentially expressed genes were randomly selected to be detected using qrt-pcr. designed by primer3 (http://fokker.wi.mit.edu/primer3/input.htm), the primer sequences were shown in . the housekeeping gene gapdh was used to correct the mrna levels of differentially expressed genes. qrt-pcr […]

2018
PMCID: 5801106
PMID: 29430376
DOI: 10.1007/s13205-018-1140-3

[…] we verified the concentration and quality of the rna samples using a nanodrop® nd-1000 spectrophotometer (nanodrop technologies, wilmington, de, usa). all pcr primers were designed using the primer3 software (https://sourceforge.net/projects/primer3/). the pcr amplification conditions were: initial denaturing for 5 min at 94 °c; followed by 35 cycles of denaturation (1 min at 95 °c), […]

2018
PMCID: 5803220
PMID: 29416074
DOI: 10.1038/s41598-018-20830-2

[…]  ). multiple sequence alignment was conducted using muscle, by including sequences of the same or closely related species obtained from genbank database (table ). primers (table ), designed using the primer3 website, were optimised and tested for cross-reactivity against the other insects used in the laboratory experiments and additional non-target invertebrates, most of them occurring in the fiel […]


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Primer3 in publications

 (7490)
PMCID: 5955877
PMID: 29769563
DOI: 10.1038/s41598-018-25389-6

[…] ranged between 30 and 400, which was considered an adequate number of hits (more is likely better). subsequently, primers targeting the most conserved region of these 16 eres were designed using primer3 software (http://bioinfo.ut.ee/primer3-0.4.0/)., in parallel, 10 of the most commonly used mouse reference genes (actb, b2m, gapdh, gusb, hprt1, polr2a, tbp, tuba1a, tubb5, and ywhaz) […]

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

[…] 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., muscle […]

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

[…] 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., total genomic […]

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

[…] alignment editor version 7.2.5 to collect detailed nucleotide information from all the different splice variants., 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 […]

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

[…] 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 […]


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

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