SP‐Designer: a user‐friendly program for designing species‐specific primer pairs from DNA sequence alignments |
| |
| Authors: | Pierre Villard Thibaut Malausa |
| |
| Institution: | 1. Institut Universitaire de Technologie de Perpignan, Département STID, Traitement des Données Génomiques, Domaine Universitaire d'Auriac, , 11000 Carcassonne, France;2. Institut National de la Recherche Agronomique, UMR ISA INRA/UNSA/CNRS, , 06903 Sophia‐Antipolis Cedex, France |
| |
| 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 . |
| |
| Keywords: | automated design identification kit software species‐specific primers |
|
|
