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Deposited research article

AutoPrime: selecting primers for expressed sequences

Gunnar Wrobel^{* 1}, Felix Kokocinski^{* 2} and Peter Lichter²

¹Divisions of Bioinformatics and Biochemistry, Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056 Basel, Switzerland

²Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany

author email corresponding author email* Contributed equally

Genome Biology 2004, 5:P11doi:10.1186/gb-2004-5-5-p11

Published:	15 April 2004

This was the first version of this article to be made available publicly.

Subject areas: Bioinformatics, Genome studies, Methods, Molecular biology

Abstract

Background

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.