Code and sample data files for performing protein motif searching

The code here is Copyright (C) 2013, Cameron Jack under the GPL v3

• protein_motif_search.py - Python script to perform motif searching.
• test_protein_motif_search.py - Python unit tests for protein_motif_search.py
• gene_common_names.txt - ENSEMBL ids with common names
• plasma_membrane_genes.txt - Example gene set pulled from ensembl.org
• plasma_membrane_out.txt - Example output
• run_protein_search.sh - Shell script to run the plasma membrane data here

You can run this with a Unix/Linux command-line as follows (where output.txt is the location you want to output the final results):

$ python protein_motif_search.py [goi_file_name] [gene_common_names.txt] [proteins.fasta] [output.txt]

You will also need to download the ENSEMBL protein sequences here: ftp://ftp.ensembl.org/pub/release-73/fasta/mus_musculus/pep/Mus_musculus.GRCm38.73.pep.all.fa.gz