Table 1

Input file parameters for MCMC-ODPR
Input parameter Default value
Genome file for BLAST searching hv_mRNA_PUT.fas
Max degeneracy (base pairs) 3
Minumum melting temperature (centigrade) 50
Maximum melting temperature (centigrade) 60
Minimum amplicon length (base pairs) 50
Maximum amplicon length (base pairs) 250
Initial overlap (base pairs) 0
Number of optimisations 10000
Maximum gap between sequences (base pairs) 10
Save interim optimizations? 0
Verbose output? 0
Cost tolerance 0
Output file name mcmc_odpr_results.out
Restart from previous run? 0
Probability of removing redundant primer pairs 0
Proportion of iterations to be considered as `early' 0
Weight greedy methods according to optimization? 1
Remove non-reusable primers from initial design? 0
Proportion of failed weight check proposals to accept (heating) 0.2

The parameters that may be input by the user into the MCMC-ODPR parameter file are in the left-most column. If the user chooses not to enter one of these parameters, then the default value on the right-most column will be used.

Kitchen et al.

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

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