Fig. 3: In silico evaluation of novel tiled primer schemes for SARS-CoV-2, BoDV-1, HAV, HEV, PV and ratHEV.
From: varVAMP: degenerate primer design for tiled full genome sequencing and qPCR
a Normalized Shannon’s entropy (1% rolling average) of the MSA used as the varVAMP input. b Number of permutations (degeneracy) of each primer in the tiled sequencing scheme for the respective viruses. Each dot shows the degeneracy of a single primer in the respective schemes (see Table 1). The horizontal lines indicate the means. (n number) Primer melting temperatures (c), hairpin temperatures (d), homo-dimer temperatures (e) and the GC content (f) were calculated either for the primer sequence including the most common nucleotides or averaged over all permutations of the final primer sequences that includes degenerate nucleotides. e, f were calculated with primer3. Each dot represents a single primer of the respective tiled schemes. The dotted lines indicate the upper target cutoffs or target ranges employed by varVAMP (nt nucleotide).
