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 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.

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"]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(DECIPHER)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: RSQLite
Loading required package: DBI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DECIPHER/deltaGrules.Rd_%03d_medium.png", width=480, height=480)
> ### Name: deltaGrules
> ### Title: Free Energy of Hybridization of Probe/Target Quadruplets on
> ###   Microarrays
> ### Aliases: deltaGrules
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(deltaGrules)
> # dG of probe = AGCT / target = A-CT pairing
> deltaGrules["A", "G", "C", "T", "A", "-", "C", "T"]
[1] 0.65071
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>