Table 2.
Results of in silico benchmarking of QuantPrime
| Primer pair specificity ranking1 | ||||||
| Species | Transcripts | Total search time | Average search time | Acceptable2 | Good3 | Very good4 |
| Arabidopsis thaliana | 5000 | 20:22:06 | 15 s | 4916 (98%) | 4323 (86%) | 2534 (50%) |
| Vitis vinifera | 5000 | 50:45:33 | 37 s | 4765 (95%) | 3927 (78%) | 2315 (46%) |
| Drosophila melanogaster | 5000 | 13:48:45 | 9.9 s | 4894 (97%) | 4075 (81%) | 3096 (61%) |
| Chlamydomonas reinhardtii | 5000 | 12:11:07 | 8.8 s | 4568 (91%) | 3999 (79%) | 2349 (46%) |
| Oryza sativa ssp japonica | 5000 | 83:31:12 | 60 s | 4658 (93%) | 3821 (76%) | 1984 (39%) |
| Hordeum vulgare | 23078 | 22:56:59 | 3.6 s | 22145 (95%) | 21564 (93%) | - |
Primer pairs designed for hypothetical high-throughput experiments, for random transcripts of each species. The numbers of successfully designed primer pairs for the different specificity ranks and the search times are reported for each species (percentages refer to the total number of transcripts tested).
1 Percentages indicate for how many of the transcripts primer pairs of at least the rank given were identified. 2 'Acceptable' amplifies only the specific sequence, but one primer has a high similarity with a non-target sequence and the primer pair might amplify genomic DNA. 3 'Good' amplifies only the target sequence, but one primer has a high similarity with a non-target sequence or the pair might amplify genomic DNA. This is the highest possible rank for primer pairs designed for species without a genome annotation. 4 'Very good' amplifies only the target sequence, both primers are highly specific to this sequence and will not amplify genomic DNA.