Table 1.
Features comparison between primer and probe selection tools most similar to PrimerHunter
| Design tool | Multiple targets | Nontargets | TM Model | Salt correction | Output |
|---|---|---|---|---|---|
| Primer3 (4) | No | Yes (DB) | NN | Yes | Multiple primer pairs |
| Insignia (9) | Yes (DB) | Yes (DB) | None | No | Multiple signatures |
| QPrimer (15) | No (DB) | No | NN | No | Multiple primers |
| DePict (14) | Yes (MSA) | No | None | No | Best primer |
| PROBEMer (8) | Yes | Yes | NN | No | Multiple probes |
| Greene SCPrimer (13) | Yes (MSA) | No | NN | Yes | Multiple primer pairs |
| OligoSpawn (16) | Yes | Yes | NN | No | Multiple probes |
| SLICSel (17) | Yes | Yes | NN | Yes | Multiple probes |
| Primaclade (18) | Yes (MSA) | No | NN | No | Multiple primers |
| OligoArray (19) | Yes | Yes (DB) | NN | No | Multiple probes |
| PrimerHunter (this article) | Yes | Yes | NN w/mismatches | Yes | Multiple primer pairs |
DB: user can select targets from a preconstructed database; MSA: input must be provided as a multiple sequence alignment; NN: nearest neighbor model.