• Top
• Abstract
• Deposited research article

As a service to the research community, Genome Biology used to publish non-peer-reviewed articles in a 'preprint' depository to which any research can be submitted and which all individuals can access free of charge.From January 2006 Genome Biology no longer publishes new articles in this section. Any article could be submitted by authors, who have sole responsibility for the article's content. The only screening process is to ensure relevance of the preprint to Genome Biology's scope and to avoid abusive, libellous or indecent articles. Articles in this section of the journal have not been peer-reviewed. Each preprint has a permanent URL, by which it can be cited. Research submitted to the preprint depository may be simultaneously or subsequently submitted to Genome Biology or any other publication for peer review; the only requirement is an explicit citation of, and link to, the preprint in the article that is eventually published. If possible, Genome Biology will provide a reciprocal link from the preprint depository to the published article.

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

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

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

The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2004/5/5/P11

Received:	13 March 2004
Posted:	15 April 2004

© 2004 BioMed Central Ltd

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.

Deposited research article

Have something to say? Post a comment on this article!