Predict oligomerization state of coiled-coil sequences.

Description

Function for predicting the oligomeric state of a coiled-coil sequence. This function allows the user to separate between antiparallel dimer, parallel dimers, trimers and higher-order coiled coils.

Usage

1
LOGICOIL(id, seq, reg, plot.result = FALSE)

Arguments

id

A string identifier for the input coiled-coil sequence.

seq

The input coiled-coil sequence, which might a string or vector of amino-acids. The input must contain at least 14 characters. Valid characters should be uppercase letters and illegal terms include ‘B’, ‘J’, ‘O’, ‘U’, ‘Z’. Invalid characters will not be tolerated and their use will result in a failure of the program. If the amino-acid in a coiled-coil sequence is unknown, it is permitted to use the identifier "X" instead

reg

The register assignments for the amino-acids in the coiled-coil sequence. The input may be either a string or a vector and must always have the same length as the seq argument. If this is not the case then the program will fail. Valid characters are the lowercase letters ‘a’ to ‘g’. Register characters are not required to be in proper order

plot.result

A logical value indicating whether the results of the predictions should be plotted on a PNG file (default=FALSE).

Value

The function LOGICOIL is the parent function in the LOGICOIL package. It is used to call the LOGICOIL prediction algorithm in order to predict the oligomeric state of a new coiled-coil sequence. The LOGICOIL function returns a vector with 4 items, which gives the odd ratio that the input sequence belongs to an antiparallel dimer, parallel, trimer or higher-order coiled coiled. If a given sequence scores f(x)==1, then there is no evidence for a particular oligomeric state. If f(x) > 1 then there is strong evidence for a particular oligimeric state, and if f(x) < 1 then there is against a particular oligimeric state.

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). DOI: 10.1093/bioinformatics/bts648

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
library(nnet)
data(pssm)
data(Model_Parameters)
data(LOGICOILfit)

score <- LOGICOIL("GCN4wt", "MKQLEDKVEELLSKNYHLENEVARLKKLV", 
  	"abcdefgabcdefgabcdefgabcdefga", plot.result=FALSE)

# print output
print(score)