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.

Kitchen et al. BMC Bioinformatics 2012 13:287   doi:10.1186/1471-2105-13-287

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