CalculateEfficiencyFISH {DECIPHER} | R Documentation

## Predict Thermodynamic Parameters of Probe/Target Sequence Pairs

### Description

Calculates the Gibbs free energy, formamide melt point, and hybridization efficiency of probe/target (DNA/RNA) pairs.

### Usage

    CalculateEfficiencyFISH(probe,
                            target,
                            temp,
                            P,
                            ions,
                            FA,
                            batchSize = 1000)

### Arguments

`probe` | A `DNAStringSet` object or character vector with unaligned probe sequences in 5' to 3' orientation.
`target` | A `DNAStringSet` object, `RNAStringSet`, or character vector with unaligned target or non-target sequences in 5' to 3' orientation. The DNA base Thymine will be treated the same as Uracil.
`temp` | Numeric specifying the hybridization temperature, typically `46` degrees Celsius.
`P` | Numeric giving the molar concentration of probes during hybridization.
`ions` | Numeric giving the molar sodium equivalent ionic concentration. Values may range between 0.01M and 1M. Note that salt correction is not available for thermodynamic rules of RNA/RNA interactions, which were determined at `1` molar concentration.
`FA` | Numeric concentration (as percent v/v) of the denaturant formamide in the hybridization buffer.
`batchSize` | Integer specifying the number of probes to simulate hybridization per batch. See the Description section below.

### Details

Hybridization of pairwise `probe`/`target` (DNA/RNA) pairs is simulated in silico. Gibbs free energies are obtained from system calls to OligoArrayAux, which must be properly installed (see the Notes section below). Probe/target pairs are sent to OligoArrayAux in batches of `batchSize`, which prevents systems calls from being too many characters. Note that OligoArrayAux does not support degeneracy codes (non-base letters), although they are accepted without error. Any sequences with ambiguity should be expanded into multiple permutations with `Disambiguate` before input.

### Value

A matrix of predicted hybridization efficiency (`HybEff`), formamide melt point (`FAm`), and free energy (`ddG1` and `dG1`) for each `probe`/`target` pair of sequences.

### Note

The program OligoArrayAux (http://www.unafold.org/Dinamelt/software/oligoarrayaux.php) must be installed in a location accessible by the system. For example, the following code should print the installed OligoArrayAux version when executed from the R console:

`system("hybrid-min -V")`

### Author(s)

Erik Wright eswright@pitt.edu

### References

ES Wright et al. (2014) "Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for Accurate Identification." Applied and Environmental Microbiology, doi:10.1128/AEM.01685-14.

### See Also

`DesignProbes`, `TileSeqs`

### Examples

    probe <- c("GGGCTTTCACATCAGACTTAAGAAACC", "CCCCACGCTTTCGCGCC")
    target <- reverseComplement(DNAStringSet(probe))
    # not run (must have OligoArrayAux installed first):
    ## Not run: CalculateEfficiencyFISH(probe, target, temp=46, P=250e-9, ions=1, FA=35)

[Package DECIPHER version 2.20.0 Index]