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Bioinformatics Advance Access published online on November 11, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti134
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 29, 2004
Revised November 1, 2004
Accepted November 2, 2004

Applications note

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

Michael D. Gadberry 1, Simon T. Malcomber 1, Andrew N. Doust 1, and Elizabeth A. Kellogg 1*

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

* To whom correspondence should be addressed.
Elizabeth A. Kellogg, E-mail: tkellogg{at}umsl.edu


  Abstract

Summary: Primaclade is a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of 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.

Availability: Primaclade can be accessed freely at www.umsl.edu/~biology/Kellogg/primaclade.html.


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