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

BMC Bioinformatics

Table 2 The variance in the number of primers obtained from 1–5x redundancy

Redundancy	Frequency of redundancy value when maximum	Number of primers > 0	Average number of primers identified	Standard error
5x	14	14	0.01	0
4x	867	881	1.28	0.03
3x	130	1005	4.39	0.05
2x	9	1020	99.54	0.1
1x	0	1020	437.41	0.22

The algorithm was repeated 1020 times with a small subset of 30 sequences. The maximum achieved redundancy obtained by MCMC-ODPR in each run was recorded and when no primers were obtained at a certain level of redundancy, a zero was added as an observation, ensuring observations at all levels of redundancy summed to 1020. Column 2 gives the number of frequency of primers found at each level of redundancy throughout all 1020 runs when their numbers were greater than none. The average number of primers identified by the algorithm each run and the standard error is presented.

ISSN: 1471-2105