MemeFinder performs the evolutionary weighting and conservation masking steps of the SLiMFinder algorithm to prepare data for input to MEME.
This page describes the uses of the MEMEFinder and MEME software for the discovery of profiles of short linear motifs over-represented in disordered regions of a set of proteins. This tool can be used to prepare input to the MEME software tool in order to weight protein sequences according to their evolutionary relatedness and mask residues that are relatively unconserved in each protein sequence.
The software is available as a commandline tool from the following address. MEME is available for download from SDSC. MEMEFinder requires a number of other freely available software tools in order to work, please cite those tools if you use them.. IUPred is a tool for the calculation of propensity for amino acids to be disordered or ordered and is used to filter out ordered residues. BLAST is used to search for homologues of protein disorder as described in the GOPHER algorithm. Clustal and Muscle are both used to draw alignments and calculate evolutionary distance between protein sequences. All these tools are freely available and should be installed before running MEMEfinder.
To run MEMEFinder you require a set of proteins, possibly identified as interacting together, that you believe are likely to share a common short linear motif. MEMEFinder generates an input file for MEME that contains the weighting and masks out domains, i.e. ordered residues, and transmembrane regions of proteins.
If you have not used IUPred before you will probably have to export some of its environmental settings to your bash profile.
python memefinder.py batch=/path/to/sequences/* usealn=T orthdb=/path/to/genome/ens_loci_proteomes.101018.fas blastpath=/path/to/blast/blast-2.2.23/bin/ iupath=/path/to/IUpred/iupred/iupred dismask=T consmask=T append=T clustalw=/path/to/clustal/clustalw2 muscle=/path/to/muscle/muscle3.8.31_i86darwin64 paralign=F usegopher=T extras=F
The memefinder program produces an output file with the suffix .dis.vec this is used as the input to MEME:
Software is available for download here:
./meme inputFile.dis.vec -minw 3 -nmotifs 100 -o ~/memeoutputdir/ -maxw 10 -protein -mod oops