Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides
Figure 3
Specificity of primers. Primers designed for all ORFs shared among each model organism used were compared against the complete set of genomes for perfect matches with oligonucleotides of the same length. Each point represents the number of perfect matches (in scale) of a primer in relation to its score. The length of the primers was 20 nucleotides. (a) Arenavirus genomes: 71 for S (small) RNA, 24 for L (large) RNA. (b) 22 Baculovirus genomes. (c) 5 Lactobacillus sp. genomes. (d) 7 Pseudomonas sp. genomes. (e) A set of primers for Lactobacillus sp. with scores between 0.85 and 0.90 were tested for nonperfect matches that could anneal unspecifically in PCR. Each bar represents the number of matches against the complete set of Lactobacillus genomes. The number below the bar indicates how many bases are shared.
