SLiMMutant is a Short Linear Motif Mutation Analysis Tool, designed to identify and assess mutations that create
and/or destroy SLiMs. There are three main run modes:
- Mode 1. Generating mutant datasets for analysis [
The main input is: (1) a file of protein sequence mutations [
mutfile=FILE] in a delimited text format with aa
mutfield=X] and protein accession number [
protfield=X] data; (2) a corresponding sequence file
seqin=FILE]; (3) a file of SLiMs to analyse [
motifs=FILE]. This will process the data and generate two sequence
*.mutant.fas. These files will be named after the input
- Mode 2. Run SLiMProb on datasets [
This will run SLiMProb on the two datasets, once per
*.ini file given by
slimini=LIST. These runs should have
runid=X settings. If no
*.ini files are given, as single run will be made using commandline settings.
- Mode 3. Compile results of SLiMProb runs. [
This will compare the
*.mutant.fas results from the
*.occ.csv file produced by SLiMProb.
All mutations analysed will be identified from
*.mutant.fas. SLiM occurrences are then matched up between wildtype
and mutant versions of the same sequence. If none of the mutations have effected the SLiM prediction, then the
wildtype and all mutant sequences will return the motif. If, on the other hand, mutations have created/destroyed
motifs, occurrences will be missing from the wildtype and/or 1+ mutant sequences. All unaffected SLiM instances are
first removed and altered SLiM instances output to
*.MutOcc.csv. Differences between mutants and wildtypes are
calculated for each
Motif combination and summary results output to
given, analysis is restricted to a subset of motifs.
basefile=FILE is given, output files will be named after
mutfile=FILE but output into the current run
directory. If running in batch mode, basefile cannot be used.
NOTE: SLiMMutant is still in development and has not been thoroughly tested or benchmarked.
SEQUENCE GENERATION METHODS
generate=T/F : Whether to run sequence generation pipeline [
mutfile=FILE : Delimited text file with sequence mutation info. Sets basefile. 
mutfield=X : Field in mutfile corresponding to AA subsitution data [
protfield=X : Field in mutfile corresponding to protein accession number [
splitfield=X : Field in mutfile to split data on (saved as basefile.X.tdt) 
seqin=FILE : Input file with protein sequences 
motifs=FILE : Input file of SLiMs 
motlist=LIST : List of input SLiMs to restrict analysis to 
mutflanks=X : Generate for
casemask=Upper of X aa flanking mutation (None if < 1) [
minmutant=X : Minimum number of mutants for output [
maxmutant=X : Maximum number of mutants for output [
SLiMProb Run Methods
slimprob=T/F : Whether to run SLiMProb on *.wildtype.fas and *.mutant.fas (*=basefile) [
slimini=LIST : Lists of INI file with settings for SLiMProb run. Should include
resdir=PATH : Location of output files. SLiMProb resdir should be in slimini [
SLiMMutant/ (and SLiMProb/)]
SLiMProb Results Analysis
analyse=T/F : Whether to analyse the results of a SLiMProb run [
resfile=FILE : Main SLiMProb results table (*.csv and *.occ.csv) [
runid=X : Limit analysis to SLiMProb RunID (blank = analyse all) 
buildpath=PATH : Alternative path to look for existing intermediate files (e.g. *.upc) [
SLiMProb PPI Analysis
slimppi=T/F : Whether to perform SLiMPPI analysis (will set
sourcepath=PATH/ : Will look in this directory for input files if not found [
sourcedate=DATE : Source file date (YYYY-MM-DD) to preferentially use [
ppisource=X : Source of PPI data. (HINT/FILE) FILE needs 'Hub' and 'SpokeUni' fields. [
dmifile=FILE : Delimited text file containing domain-motif interaction data [
batch=FILELIST : List of mutfiles to run in batch mode. Wildcards allowed. 
See also rje.py generic commandline options.
History Module Version History
# 0.0 - Initial Compilation.
# 1.0 - Working version with standalone functionality.
# 1.1 - Minor tweaks to generate method to increase speed. (Make index in method.) Added splitfield=X.
# 1.2 - Added a batch mode for mutfiles - all other options will be kept fixed. Added maxmutant and minmutant.
# 1.3 - Added SLiMPPI analysis (will set analyse=T). Started basing on SLiMCore