AmplifyDNA(primers, myDNAStringSet, maxProductSize, annealingTemp, P, ions = 0.2, includePrimers=TRUE, minEfficiency = 0.001, ...)DNAStringSet object or character vector with one or more unaligned primer sequences in 5' to 3' orientation.
DNAStringSet object or character vector with unaligned template DNA sequences in 5' to 3' orientation.
0.1%). (See details section below.)
CalculateEfficiencyPCR, including batchSize, taqEfficiency, maxDistance, maxGaps, and processors.
DNAStringSet object containing potential PCR products, sorted from highest-to-lowest amplification efficiency. The sequences are named by their predicted amplification efficiency followed by the index of each primer in myDNAStringSet. (See examples section below.)
AmplifyDNA first searches for primer target sites on the template DNA, and then calculates an amplification efficiency from each target site using CalculateEfficiencyPCR. Ambiguity codes (IUPAC_CODE_MAP) are supported in the primers, but not in myDNAStringSet to prevent trivial matches (e.g., runs of N's).If taqEfficiency is TRUE (the default), the amplification efficiency of each primer is defined as the product of hybridization efficiency and elongation efficiency. Amplification efficiency must be at least minEfficiency for a primer to be amplified in silico. Overall amplification efficiency of the PCR product is then calculated as the geometric mean of the two (i.e., forward and reverse) primers' efficiencies. Finally, amplicons are generated if the two primers are within maxProductSize nucleotides downstream of each other.
Potential PCR products are returned, either with or without including the primer sequences in the amplicon. The default (includePrimers=TRUE) is to incorporate the primer sequences as would normally occur during amplification. The alternative is to return the complete template sequence including the target sites, which may not exactly match the primer sequences. Note that amplicons may be duplicated when different input primers can amplify the same region of DNA.
CalculateEfficiencyPCR, DesignPrimers, DesignSignatures, MeltDNA
data(yeastSEQCHR1)
# not run (must have OligoArrayAux installed first):
# match a single primer that acts as both the forward and reverse
primer1 <- "TGGAAGCTGAAACG"
## Not run: AmplifyDNA(primer1, yeastSEQCHR1, annealingTemp=55, P=4e-7, maxProductSize=500)
# perform a typical amplification with two primer sequences:
primer2 <- c("GGCTGTTGTTGGTGTT", "TGTCATCAGAACACCAA")
## Not run: AmplifyDNA(primer2, yeastSEQCHR1, annealingTemp=55, P=4e-7, maxProductSize=500)
# perform a multiplex PCR amplification with multiple primers:
primers <- c(primer1, primer2)
## Not run: AmplifyDNA(primers, yeastSEQCHR1, annealingTemp=55, P=4e-7, maxProductSize=500)
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