MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling

BMC Bioinformatics

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.

ISSN: 1471-2105