DECIPHER (version 2.0.2)

deltaGrules: 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" ...

Source

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

Details

The first four dimensions correspond to the 4 probe positions from 5' to 3'. The fifth to eighth dimensions correspond to the 4 positions from 5' to 3' of the target sequence.

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"]