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Bioinformatics Advance Access originally published online on November 11, 2004
Bioinformatics 2005 21(7):1263-1264; doi:10.1093/bioinformatics/bti134
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

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

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

*To whom correspondence should be addressed.

Summary: 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.

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

Contact: tkellogg{at}umsl.edu


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