Predict oligomerization state of coiled-coil sequences.

Description

Functions for predicting the oligomeric state of user-defined coiled-coil sequencse. Those functions allow the user to separate between antiparallel dimer, parallel dimers, trimers and higher-order coiled coils.

Details

Functions in the LOGICOIL package allow users to apply the LOGICOIL prediction algorithm to predict the oligomeric state of coiled-coil sequences.

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

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

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

# print output
print(score)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LOGICOIL)
Loading required package: nnet
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LOGICOIL/LOGICOIL-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LOGICOIL-package
> ### Title: Predict oligomerization state of coiled-coil sequences.
> ### Aliases: LOGICOIL-package
> 
> ### ** Examples
> 
> library(nnet)
> data(pssm)
> data(Model_Parameters)
> data(LOGICOILfit)
> 
> score <- LOGICOIL("GCN4wt", "MKQLEDKVEELLSKNYHLENEVARLKKLV", 
+     "abcdefgabcdefgabcdefgabcdefga", plot.result=TRUE)
Estimating oligomeric state of coiled-coil sequences
Analysis complete!
> 
> # print output
> print(score)
        1         2         3         4 
0.6951839 1.5669293 0.5670830 2.0606170 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>