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.