Two primer design programs, RJPrimers and BatchPrimer3, which were hosted by GrainGenes, are now available through the GrainGenes' "GrainGenes Tools" menu.

RJPrimers (https://probes.pw.usda.gov/RJPrimers/) is a program based on transposable element junction-based PCR primer design. Reference: Frank M. You, Humphrey Wanjugi, Naxin Huo, Gerard R. Lazo, Ming-Cheng Luo, Olin D. Anderson, Jan Dvorak and Yong Q. Gu. RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development. Nucleic Acids Research, 2010, Web Server Issue. doi:10.1093/nar/gkq425. [NAR: https://academic.oup.com/nar/article/38/suppl_2/W313/1111009]

BatchPrimer3 (https://probes.pw.usda.gov/batchprimer3/index.html) is a high throughput web application for PCR and sequencing primer design. Reference: Frank M You, Naxin Huo, Yong Qiang Gu, Ming-cheng Luo, Yaqin Ma, Dave Hane, Gerard R Lazo, Jan Dvorak and Olin D Anderson. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008, 9:253, doi:10.1186/1471-2105-9-253 [PubMed: https://pubmed.ncbi.nlm.nih.gov/18510760/]