Design of specie-specific primers for virus diagnosis in plants with PCR

We propose a specialist software to diagnose viral disease in plants. Our strategy is to align nucleotide sequences of plant virus to discover specie-specific regions of genes of the viral genomes, so as to design a primer. The program designs oligo-nucleotide primers used for polymerase chain reaction (PCR), a very cheap diagnosis technique. The user can specify (or use default) constraints for primer and amplified product lengths, as percentage of G+C, absolute or relative melting temperatures, and primer 3´ nucleotides. The program screens candidate primer sequences with displayed user-specifiable parameters in order to help minimizing nonspecific priming and primer secondary structure. We tested this tool by designing two specific primers which were used to amplify known viral species, then used to perform a virus diagnosis.