Plot the LOGICOIL scores

Share:

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

1
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.

Details

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

Value

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

Author(s)

Thomas L. Vincent tlfvincent@gmail.com

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
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")