title: SP-Designer: a user-friendly program for designing species-specific primer pairs from DNA sequence alignments.
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.
authors: Institut Universitaire de Technologie de Perpignan, Département STID, Traitement des Données Génomiques, Domaine Universitaire d'Auriac, Carcassonne, France.
authors: Pierre
authors: P
authors: Villard
authors: Thibaut
authors: T
authors: Malausa
mesh_terms: D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers / Q000235:genetics*; D008967:Molecular Biology / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D016415:Sequence Alignment; D012984:Software
chemical_list: D017931:DNA Primers