Table 1 Input file parameters for MCMC-ODPR
From: MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling
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 |