deltaGrules {DECIPHER} | R Documentation

## Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays

### Description

An 8D array with four adjacent base pairs of the probe and target sequences at a time. Each dimension has five elements defining the residue at that position ("A", "C", "G", "T", or "-"). The array contains the standard Gibbs free energy change of probe binding (dG, [kcal/mol]) for every quadruple base pairing.

### Usage

    data(deltaGrules)

### Format

The format is: num [1:5, 1:5, 1:5, 1:5, 1:5, 1:5, 1:5, 1:5] -0.141 0 0 0 0 ... - attr(*, "dimnames")=List of 8 ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ...

### Details

The first four dimensions correspond to the four probe positions from 5' to 3'. The fifth to eighth dimensions correspond to the four positions from 5' to 3' of the target sequence.

### Source

Data obtained using NimbleGen microarrays and a Linear Free Energy Model developed by Yilmaz et al.

### References

Yilmaz LS, Loy A, Wright ES, Wagner M, Noguera DR (2012) Modeling Formamide Denaturation of Probe-Target Hybrids for Improved Microarray Probe Design in Microbial Diagnostics. PLoS ONE 7(8): e43862. doi:10.1371/journal.pone.0043862.

### Examples

    data(deltaGrules)
    # dG of probe = AGCT / target = A-CT pairing
    deltaGrules["A", "G", "C", "T", "A", "-", "C", "T"]

[Package DECIPHER version 2.22.0 Index]