PrimerSeq designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. PrimerSeq is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. PrimerSeq incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for your particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for your data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species.


New! PrimerSeq is now version 1.1
Windows and Mac OS X downloads are available


Tokheim C., Park JW., Xing Y. (2014) PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data, Genomics, Proteomics & Bioinformatics, 12(2):105-109. [journal]


Click here for the windows or here for the Mac OS X installation guide. You should have the Java JRE (Windows, Mac OS X), possibly already, installed.