Table 4

Performance of primer design software for multiple sequence input
Program Number of primers designed Cost (nucleotides) Coverage (bp) Percentage coverage Cost per covered base (nucleotides) Execution time (minutes)*
MCMC-ODPR 1521(1786) 30103 162196 77.37 0.19 637
BatchPrimer3 372(1153) 15427 62292 29.71 0.25 2.98
PAMPS 1205(13598) 25284 39240 18.72 0.64 5.19

MCMC-ODPR was run with 184 sequences for 10,000 iterations with the cost per bases covered and runtime was used as a comparison statistic for performance. MCMC_ODPR outperformed multiple sequence input programs BatchPrimer3 and PAMPS in terms of cost per bases covered, yet was clearly slower in terms of runtime.

Total number of primer sites identified shown in parentheses.

* MCMC-ODPR Execution was performed on a 2.26 GHz Intel® Core 2 Duo MacBook running Mac OS X version 10.6.8 with 2 GB RAM. Execution time for BatchPrimer 3 was provided by the BatchPrimer3 web server (primer design server 1) found at http://probes.pw.usda.gov/batchprimer3/ webcite. Execution for PAMPS was performed on a 2.31 GHz AMD Phenomtm 8650 Triple-Core Processor PC running Windows XP with 3.5 GB of RAM.

Kitchen et al.

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

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