Research Article
Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes
Table 3
Number of nontarget amplicons predicted in a multiplex reaction of tiled primers for 3 kb amplicons. In a multiplex of the 3 kb-amplicon tiled primers for a given organism, of the possible reactions producing products, only a small number of primer combinations are predicted to amplify regions in nontarget organisms. Counts show the number of unique primer combinations in a multiplex that yield products for any sequence in the NCBI nt nucleotide database. The numerator is for any nontarget organism in nt and the denominator is for any target or nontarget organism in nt, that is, nonspecific/total of the possible primer combinations in the multiplex predicted to yield product when compared against nt. Vastly more amplicons are produced from target organisms, indicating any contaminating nontarget species should be a small minority of amplified product.
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