Table 3 |
|||||||
| Performance of primer design software for single sequence input | |||||||
| Program | Size of gene (bp) | Number of primers in design | Cost (nucleotides) | Coverage (bp) | Percentage coverage | Cost per covered base (nucleotides) | |
| Dehydrin 9 | Primer3 | 1000 | 4(18) | 80 | 401 | 40.1 | 0.2 |
| Primer-BLAST | 1000 | 6(12) | 116 | 527 | 52.7 | 0.22 | |
| MCMC-ODPR | 1000 | 9(10) | 197 | 958 | 95.8 | 0.21 | |
| Beta-amylase 1 | Primer3 | 3733 | 10(66) | 160 | 691 | 18.51 | 0.23 |
| Primer-BLAST | 3733 | 14(36) | 334 | 998 | 26.73 | 0.33 | |
| MCMC-ODPR | 3733 | 34(34) | 682 | 3636 | 97.4 | 0.19 | |
| C-repeat binding factor 3 like protein | Primer3 | 1515 | 8(26) | 160 | 487 | 32.15 | 0.33 |
| Primer-BLAST | 1515 | 6(14) | 120 | 473 | 31.22 | 0.25 | |
| MCMC-ODPR | 1515 | 14(14) | 274 | 1500 | 99.01 | 0.18 | |
MCMC was input with one sequence corresponding to one gene (first column) and run for 10,000 iterations. The cost per bases covered in nucleotides was used as a comparison of performance. MCMC-ODPR performs less optimally with one sequence, yet was able to outperform single sequence programs Primer3 and Primer-BLAST in all examples but one.
Total number of primer sites identified shown in parentheses.
Kitchen et al. BMC Bioinformatics 2012 13:287 doi:10.1186/1471-2105-13-287
