BatchPrimer3 specifications


Unique identifier OMICS_02370
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

BatchPrimer3 article

BatchPrimer3 citations

PMCID: 5605536

[…] fold change ≥2., to support the efficacy of gene expression in rna-seq analysis, key genes of sgs and gas biosynthesis were selected for qrt-pcr validation. gene specific primers were designed using batchprimer3 ( and their related information is listed in table s9. total rna was isolated from leaf tissues of respective phases (lv, lb and lf) followed […]

PMCID: 5551020

[…] of the eight sub-sampled data sets., a total of 16 snps called with a minimum sequence depth of 56 per locus per sample (table 2) were randomly selected for validation. primers were designed using batchprimer3 v1.0 ( from sorghum genome harboring the snps. only the primers with one alignment to the sorghum genome 3.0 [21] and alignment to sugarcane […]

PMCID: 4757707

[…] and tobacco anthocyanin biosynthetic genes were analyzed using quantitative real-time pcr (qrt-pcr) as described previously (lai et al., 2014). the specific qrt-pcr primers were designed using a batchprimer3 program listed in supplementary table s2 (you et al., 2008). using these gene-specific primers, each assay amplified a single product of the correct size and demonstrated an acceptable […]

PMCID: 4751557

[…] (li et al., 2009)., allele-specific forward primers and a common reverse primer were designed for use in kasp (kompetitive allele specific pcr) assays (lgc genomics ltd. hoddesdon, u.k.), using batchprimer3 ( with the “allele specific primers and allele flanking primers” option. the parameter used were 60–120 bp in size, tm between 58–60° and gc […]

PMCID: 4535569

[…] singletons containing trinucleotide repeat microsatellite repeats were extracted from this .fasta file using the script, and output into a separate .fasta file, and used as input for batchprimer3 using the ssr screening and design option (program available at, to verify the utility of microsatellite markers, we used the s. […]

BatchPrimer3 institution(s)
Department of Plant Sciences, University of California, CA, USA

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