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Nucleic Acids Research Advance Access originally published online on April 28, 2009
Nucleic Acids Research 2009 37(Web Server issue):W209-W213; doi:10.1093/nar/gkp269
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W209-W213
© 2009 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.

Articles

UniPrime2: a web service providing easier Universal Primer design

Robin Boutros1, Nicola Stokes1, Michaël Bekaert2 and Emma C. Teeling2,*

1UCD School of Computer Science and Informatics and 2UCD School of Biology and Environmental Science & UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland

*To whom correspondence should be addressed. Tel: +353 1 716 2263; Fax: +353 1 716 1152; Email: emma.teeling{at}ucd.ie

Received January 31, 2009. Revised April 3, 2009. Accepted April 11, 2009.

The UniPrime2 web server is a publicly available online resource which automatically designs large sets of universal primers when given a gene reference ID or Fasta sequence input by a user. UniPrime2 works by automatically retrieving and aligning homologous sequences from GenBank, identifying regions of conservation within the alignment, and generating suitable primers that can be used to amplify variable genomic regions. In essence, UniPrime2 is a suite of publicly available software packages (Blastn, T-Coffee, GramAlign, Primer3), which reduces the laborious process of primer design, by integrating these programs into a single software pipeline. Hence, UniPrime2 differs from previous primer design web services in that all steps are automated, linked, saved and phylogenetically delimited, only requiring a single user-defined gene reference ID or input sequence. We provide an overview of the web service and wet-laboratory validation of the primers generated. The system is freely accessible at: http://uniprime.batlab.eu. UniPrime2 is licenced under a Creative Commons Attribution Noncommercial-Share Alike 3.0 Licence.


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