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Bioinformatics. 2005 Apr 1;21(7):1263-4. Epub 2004 Nov 11.

Primaclade--a flexible tool to find conserved PCR primers across multiple species.

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  • 1Department of Biology, University of Missouri-St. Louis, One University Boulevard, St. Louis, MO 63121, USA.


Primaclade is a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of polymerase chain reaction (PCR) primers that will bind across the alignment. Primaclade iteratively runs the Primer3 application for each alignment sequence and collates the results. Primaclade creates an HTML results page that recaps the original alignment, provides a consensus sequence and lists primers for each alignment area, with primers color-coded to reflect the level of degeneracy in the primer.

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