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SP-Designer: a user-friendly program for designing species-specific primer pairs from DNA sequence alignments

Authors

  • Pierre Villard,

    1. Institut Universitaire de Technologie de Perpignan, Département STID, Traitement des Données Génomiques, Domaine Universitaire d'Auriac, Carcassonne, France
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  • Thibaut Malausa

    Corresponding author
    1. Institut National de la Recherche Agronomique, UMR ISA INRA/UNSA/CNRS, Sophia-Antipolis Cedex, France
    • Institut Universitaire de Technologie de Perpignan, Département STID, Traitement des Données Génomiques, Domaine Universitaire d'Auriac, Carcassonne, France
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Correspondence: Thibaut Malausa, Fax: 33 4 92386401; E-mail: tmalausa@sophia.inra.fr

Abstract

SP-Designer is an open-source program providing a user-friendly tool for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. SP-Designer selects PCR primer pairs for the amplification of DNA from a target species on the basis of several criteria: (i) primer specificity, as assessed by interspecific sequence polymorphism in the annealing regions, (ii) the biochemical characteristics of the primers and (iii) the intended PCR conditions. SP-Designer generates tables, detailing the primer pair and PCR characteristics, and a FASTA file locating the primer sequences in the original sequence alignment. SP-Designer is Windows-compatible and freely available from http://www2.sophia.inra.fr/urih/sophia_mart/sp_designer/info_sp_designer.php.

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