slimR is a protein sequence analysis package centered around short linear motifs (SLiMs) and their connections to human diseases. The package contains functions to retrieve data from public databases such as ELM (elm.eu.org), UniProt (uniprot.org), PFAM, and Clinvar. Annotated SLiMs and SLiM patterns (regular expressions) are retrieved from the ELM database. Protein sequence features such as disease-causing mutations, polymorphisms, protein domains, and many other annotated features are retrieved from the UniProt database. The main motivation of the package is to facilitate analysis of the impact of protein sequence variations due to mutations and polymorphism on the content of SLiMs. Besides functions to retrieve data from public resources, there are functions to calculate disorder scores, search for SLiM instances in given sequences, look for gain/loss of SLiMs due to sequence variations. The package should be useful not only for the analysis of human diseases but also studies of the evolution of species via gain/loss of SLiMs in any comparative context.
The package can be installed via github using R library devtools.
install.packages('devtools')
devtools::install_github('BIMSBbioinfo/slimR')
The following command installs the latest version of the R package from Anaconda.
conda install -c bora.uyar r-slimr
Currently, the package depends on IUPred tool for sequence disorder score prediction. IUPred source code can be dowloaded from here: http://iupred.enzim.hu/Downloads.php After unpacking the source code, change to the src directory. Compile the code with "cc iupred.c -o iupred". Some of the functions will require the path to the folder that contains the iupred executable