BatchPrimer3 pipeline

BatchPrimer3 specifications

Information


Unique identifier OMICS_02370
Name BatchPrimer3
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability No
Maintained No

Publication for BatchPrimer3

BatchPrimer3 IN pipelines

 (8)
2017
PMCID: 5363057
PMID: 28330454
DOI: 10.1186/s12864-017-3643-4

[…] gt, gh_e22 vs. gm and gh_e22 vs. gd were randomly selected to design flanking primers. these flanking primers were designed from the 150 bp flanking sequences of the 40 randomly selected snps using batchprimer3 [53] with an optimal annealing temperature of 57 °c, optimal product size of 200 bp and the remaining parameters at their default settings. the designed primers were synthesized […]

2017
PMCID: 5605536
PMID: 28928460
DOI: 10.1038/s41598-017-12025-y

[…] 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 (http://probes.pw.usda.gov/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 […]

2017
PMCID: 5605536
PMID: 28928460
DOI: 10.1038/s41598-017-12025-y

[…] 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 (http://probes.pw.usda.gov/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 by removal of genomic dna contamination […]

2016
PMCID: 4757707
PMID: 26925082
DOI: 10.3389/fpls.2016.00166

[…] 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 […]

2015
PMCID: 4535569
PMID: 26163593
DOI: 10.1093/jisesa/iev069

[…] singletons containing trinucleotide repeat microsatellite repeats were extracted from this .fasta file using the script selectseqs.pl, and output into a separate .fasta file, and used as input for batchprimer3 using the ssr screening and design option (program available at http://probes.pw.usda.gov/batchprimer3/index.html)., 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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