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Nucleic Acids Research Advance Access published online on April 19, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn191
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

UniPrime: a workflow-based platform for improved universal primer design

Michaël Bekaert* and Emma C. Teeling

School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland

*To whom correspondence should be addressed. Tel: +353 1 716 2263; Fax: +353 1 716 1152; Email: michael{at}batlab.eu

Received December 18, 2007. Revised March 19, 2008. Accepted April 1, 2008.

UniPrime is an open-source software (http://uniprime.batlab.eu), which automatically designs large sets of universal primers by simply inputting a gene ID reference. UniPrime automatically retrieves and aligns homologous sequences from GenBank, identifies regions of conservation within the alignment and generates suitable primers that can amplify variable genomic regions. UniPrime differs from previous automatic primer design programs in that all steps of primer design are automated, saved and are phylogenetically limited. We have experimentally verified the efficiency and success of this program by amplifying and sequencing four diverse genes (AOF2, EFEMP1, LRP6 and OAZ1) across multiple Orders of mammals. UniPrime is an experimentally validated, fully automated program that generates successful cross-species primers that take into account the biological aspects of the PCR.


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