Primer-BLAST specifications


Unique identifier OMICS_02343
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


  • person_outline Jian Ye <>

Primer-BLAST article

Primer-BLAST citations

PMCID: 5841425

[…] 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 […]

PMCID: 5807760

[…] bioinformatics tool, primer bank ( [69–71]. the primers were further justified in the ncbi primer designing tool ( 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 […]

PMCID: 5780484

[…] for qpcr, using prime script tm rt reagent kit with gdna eraser (takara, dalian, china). specific primers for qpcr were designed using premier primer 5 (supplementary table s1) and verified by ncbi primer-blast. elongation factor was used as an endogenous control29. the amplification was performed on the lightcycler 480 real-time pcr instrument (roche diagnostics, burgess hill, uk) using sybr® […]

PMCID: 5772385

[…] 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 […]

PMCID: 5742884

[…] were randomly selected to validate the results of rna-seq by rt-qpcr. 1 μg of total rna was reverse transcribed to cdna in 20 μl reaction. custom gene-specific primers for qrt-pcr were designed by primer-blast, and the sequences of primers are listed in table 1. gene expression was measured in triplicates using the abi steponeplus® instrument (abi, usa) and sybr greenimaster mix (roche, usa). […]

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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