UniPrime2 is an experimentally validated, fully automated program that generates successful cross-species primers that take into account the biological aspects of the PCR. UniPrime2 automatically retrieves and aligns orthologous sequences from GenBank, identifies regions of conservation within the alignment and generates suitable primers that can amplify variable genomic regions. UniPrime2 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.
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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W209-13. Epub 2009 Apr 28.
UniPrime2: a web service providing easier Universal Primer design.
Boutros R, Stokes N, Bekaert M, Teeling EC.