Primer-BLAST pipeline

Primer-BLAST specifications

Information


Unique identifier OMICS_02343
Name Primer-BLAST
Interface Web user interface
Restrictions to use None
Input data Accession, gi, or sequence
Input format FASTA
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jian Ye <>

Publication for Primer-BLAST

Primer-BLAST IN pipelines

 (39)
2018
PMCID: 5772385
PMID: 29362695
DOI: 10.7717/peerj.4261

[…] nnotations related to gene regulation, immune response, and growth (table 1). corresponding contigs were then selected from the transcriptome using the seqinr package (charif & lobry, 2007). ncbi primer blast was used to develop primers for qpcr using the following parameters: amplicon size 100–400 bp, gc content 55–60%, melt temperatures ∼60 °c and within 0.5 °c of each other, self and 3′ com […]

2018
PMCID: 5807760
PMID: 29426343
DOI: 10.1186/s12989-018-0244-6

[…] bioinformatics tool, primer bank (https://pga.mgh.harvard.edu/primerbank/index.html) [69–71]. the primers were further justified in the ncbi primer designing tool (https://www.ncbi.nlm.nih.gov/tools/primer-blast/) ye et al., [72]. the forward and reverse primers of the corresponding gene were listed in table 1.table 1primersnamesequencebax forwardccc gag agg tct ttt tcc gagbax reversecca gcc cat […]

2018
PMCID: 5841425
PMID: 29515101
DOI: 10.1038/s41419-018-0421-4

[…] pcr system (applied biosystems, foster city, ca, usa). relative quantification was based on the δδct method, and rplp0 gene was used as a reference control. pcr primers were designed using ncbi primer-blast., rna sequencing libraries were prepared using the illumina truseq sample preparation kit and sequenced on a hiseq 2000 system (illumina, san diego, ca, usa), according […]

2018
PMCID: 5859231
PMID: 29593755
DOI: 10.3389/fpls.2018.00283

[…] at primer sites. the designed primers were analyzed using the idt oligoanalyzerv3.1 tools5 for the primer properties, hairpins and self/cross hybridization. the primers were verified using the primer-blast ncbi to ensure specificity and were synthesized through eurofins analytical services india pvt. ltd. (bangalore, india)., real-time pcr amplification followed by dna melting […]

2017
PMCID: 5286434
PMID: 28145408
DOI: 10.1038/srep39069

[…] rneasy plant mini kit (qiagen inc, ca, usa). the cdna was synthesized using the maxima h minus first strand cdna synthesis kit (thermo fisher scientific inc.). the qpcr primers were designed using primer-blast and listed in supplemental table 2. three biological replicates and three technical replicates for each sample were performed. the δctmean was calculated using normalization […]

Primer-BLAST institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Neuroscience and Behavioral Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore
Primer-BLAST funding source(s)
Supported by the Intramural Research Program of the NIH, National Library of Medicine, the Singapore Ministry of Health and the Agency for Science, Technology, and Research.

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