LOGICOIL (version 0.99.0)

plot_LOGICOIL: Plot the LOGICOIL scores

Description

This function can be used to plot the results of applying the LOGICOIL prediction algorithm to user-defined coiled-coil sequences. The plot helps visualize the LOGICOIL scores at each position of the coiled-coil sequence.

Usage

plot_LOGICOIL(prob.oligo, id)

Arguments

prob.oligo

A matrix of dimension n x 4, where n is the length of the input coiled-coil sequence, and each column represents the LOGICOIL scores for antiparallel dimer, parallel, trimer and higher-order coiled coiled.

id

A string that represents the id name of the input sequence.

Value

A PNG file that shows the LOGICOIL prediction scores at each of the position of the input coiled-coil sequence.

Details

The required input for this function can be obtained by running the EstimateProbability function (see example).

References

Thomas L. Vincent, Peter J. Green and Dek N. Woolfson. "LOGICOIL-multi-state prediction of coiled-coil oligomeric state", 29(1), pp69-76, Bioinformatics, (2013).

Examples

library(nnet)
data(pssm)
data(Model_Parameters)
data(LOGICOILfit)

cat("Estimating oligomeric state of coiled-coil sequences\n")
prob.oligo <- EstimateProbability("GCN4wt",
  "MKQLEDKVEELLSKNYHLENEVARLKKLV",
  "abcdefgabcdefgabcdefgabcdefga",
  pssm,
  LOGICOILfit,
  Model_Parameters)

# plot LOGICOIL results obtained from user-defined coiled-coil sequences
plot_LOGICOIL(prob.oligo, "GCN4wt")