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.
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.
A string that represents the id name of the input sequence.
The required input for this function can be obtained by running the
EstimateProbability function (see example).
A PNG file that shows the LOGICOIL prediction scores at each of the position of the input coiled-coil sequence.
Thomas L. Vincent [email protected]
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).
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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")
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