runIUPred: runIUPred

In BIMSBbioinfo/slimR: Short Linear Motif (SLiM) Analysis in the context of human diseases

Description

run IUPred tool to get disorder propensity scores of a given protein sequence in fasta format.

Usage

runIUPred(iupredPath, fastaFile, nodeN = 1)

Arguments

iupredPath	The path to the folder containing the source code of the IUPred tool
fastaFile	A fasta file containing the amino acid sequences
nodeN	default: 1. Positive integer for the number of parallel cores to use for downloading and processing the files

Details

Given a fasta file containing one or more protein sequences; calculate per-base iupred disorder scores. IUPred source code can be dowloaded from here: http://iupred.enzim.hu/Downloads.php After unpacking the source code, cd to the src directory. Compile the code with "cc iupred.c -o iupred"

Value

A list of numerical arrays, where each value in the array correspond to the disorder score propensity of the corresponding residue in the protein sequence.

Examples

## Not run: 
glutFastaFile <- system.file("extdata", "glut.fasta", package = 'slimR')
#get disorder scores
iupred <- runIUPred('/home/buyar/tools/iupred/', glutFastaFile, 1)
#plot disorder score profile
plot(iupred[[1]], col = ifelse(iupred[[1]] > 0.4, 'red', 'black'), main = names(iupred)[1])

## End(Not run)

BIMSBbioinfo/slimR documentation built on Nov. 4, 2021, 6:48 a.m.