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Table 4 Performance of primer design software for multiple sequence input

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

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

  1. 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.
  2. Total number of primer sites identified shown in parentheses.
  3. * 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 athttp://probes.pw.usda.gov/batchprimer3/. 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.
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BMC Bioinformatics

ISSN: 1471-2105

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