QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR

BMC Bioinformatics

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.

ISSN: 1471-2105