Applied Bioinformatics

, Volume 5, Issue 2, pp 119–120 | Cite as


Automated Primer Design for Exon Sequences
Application Note


EasyExonPrimer is a web-based software that automates the design of PCR primers to amplify exon sequences from genomic DNA. EasyExonPrimer is written in Perl and uses Primer3 to design PCR primers based on the genome builds and annotation databases available at the University of California, Santa Cruz (UCSC) Genome Browser database ( It masks repeats and known single nucleotide polymorphism (SNP) sites in the genome and designs standardised primers using optimised conditions. Users can input genes by RefSeq mRNA ID, gene name or keyword. The primer design is optimised for large-scale resequencing of exons. For exons larger than 1kb, the user has the option of breaking the exon sequence down into overlapping smaller fragments. All primer pairs are then verified using the In-Silico PCR software to test for uniqueness in the genome. We have designed >1000 pairs of primers for 90 genes; 95% of the primer pairs successfully amplified exon sequences under standard PCR conditions without requiring further optimisation.


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Copyright information

© Adis Data Information BV 2006

Authors and Affiliations

  1. 1.Laboratory of Molecular Technology, Scientific Application International Corporation - FrederickNational Cancer Institute at FrederickFrederickUSA

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