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

Authors: Gadberry, Michael D.; Malcomber, Simon T.; Doust, Andrew N.; Kellogg, Elizabeth A.

Source: Bioinformatics, Volume 21, Number 7, 01 April 2005 , pp. 1263-1264(2)

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Abstract:

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@umsl.edu

Document Type: Research article

DOI: http://dx.doi.org/10.1093/bioinformatics/bti134

Affiliations: 1: *To whom correspondence should be addressed.

Publication date: 2005-04-01

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The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.