TABLE 2.
CIRCprimerXL web tool parameters. CIRCprimerXL takes multiple parameters to adjust the species, input template and amplicon size, GC ant Tm primer settings, SNP, and specificity evaluation.
| Parameter | Default | Options |
|---|---|---|
| species | human | human, mouse, rat, zebrafish, Xenopus tropicalis, or Caenorhabditis elegans |
| Of note, the SNP filter is only activated when designing primers for human circRNAs | ||
| splicing | yes | yes: the template sequence is spliced |
| no: the template sequence is not spliced | ||
| template length | 150 (which results in a total template length of 300 nucleotides) | any integer between 50 and 500 |
| amplicon length | calculated based on template length | any integer between 50 and 500 |
| primer GC settings | 30-50-80 (minimum—optimum—maximum) | any integer between 15 and 85 |
| primer Tm settings | 58-59-60 (minimum—optimum—maximum) | any integer between 50 and 70 |
| SNP filter | strict | strict: avoids common SNPs in primer design |
| loose: avoids common SNPs in the 3′ end half of primer | ||
| off-targets filter | strict | strict or loose (see Table 1) |