Table 2 Main features of similar web-based primer design tools
From: TipMT: Identification of PCR-based taxon-specific markers
| Tool | Sequence input | Search for Target sequences | Specificity check method | Output | Multiplex check |
|---|---|---|---|---|---|
| BatchPrimer3 | multiple sequences (up to 500) |
yes (SSR, SNP) | none | primers information | no |
| jPCR | multiple sequences |
yes (SSR only) | alignment | primers information | yes |
| MPprimer | multiple sequences | no |
thermodynamic (limited and pre-defined list of sequences) | primers information and virtual gel | yes |
| TipMT | multiple sequences from multiple taxa |
yes (SSR, orthologs, singletons) | alignment and thermodynamic | primers information and virtual gel | yes |