PCR Amplicon Prediction from Multiplex Degenerate Primer and Probe Sets

Software · Thu Aug 08 00:00:00 EDT 2013

DOI:https://doi.org/10.11578/dc.20200930.8· OSTI ID:1231672 · Code ID:45125

Gardner, S. N.

Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. Code is described to predict potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons.

• Short Name / Acronym: Simulate PCR, v1.0
• Project Type: Open Source, No Publicly Available Repository
• Site Accession Number: LLNL-CODE-642995; 5024
• Software Type: Scientific
• License(s): BSD 3-clause "New" or "Revised" License
• Programming Language(s): PERL
• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
• Sponsoring Organization: USDOE

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  Primary Award/Contract Number:

  AC52-07NA27344
• DOE Contract Number: AC52-07NA27344
• Code ID: 45125
• OSTI ID: 1231672
• Country of Origin: United States