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  • Deposited research article
  • Open Access

AutoPrime: selecting primers for expressed sequences

Contributed equally
Genome Biology20045:P11

  • Received: 13 March 2004
  • Published:



Primers designed for expressed sequences should be specific for the mRNA sequence of a gene but not yield a product from its genomic sequence. Already slight contaminations of genomic DNA can lead to incorrect measurements for sensitive methods like real-time PCR (RT-PCR).

Results and Conclusions

The software AutoPrime automates the task of generating such primers for RT-PCR experiments by combining the information from sequence databases with primer design software. Thus the software is able to cope with the high demand of RT-PCR validation experiments following the recent increase in microarray expression profiling studies. The software generates high quality primers more efficiently than possible by manual design methods and has been successfully employed for RT-PCR primer design in our as well as other laboratories.


  • Primer Design
  • Ensembl Database
  • Genome Biology
  • Perl Module
  • Adjacent Exon