A Catalog of the Diversity and Ubiquity of Bacterial Microcompartments
Scripts and example data
uniprot_to_fasta_annotated.py convert Uniprot text file to fasta format, extracting gene id, pfams, taxid and accession and stores it in the fasta header example: ./uniprot_to_fa_annotated.py example_data/Hoch_5814.txt > Hoch_5814.fa
locus_fasta_to_signature_and_diagram.py runs hmms against locus in fasta format (with extra information in fasta header), creates a short signature and visualizes the locus example: ./locus_fasta_to_signature_and_diagram.py example_data/ACI/A3B65__locus_1_main_sat.fa ACI > out.sig
compare_locus_signatures.py uses the locus signatures from all BMC loci (or a subset) to compare them against each other, output is tab separated for import into Cytoscape example: ./compare_locus_signatures.py example_data/SPU_loci_signatures.txt > out.tsv
Dependencies
biopython 1.78: pip3 install biopython (https://biopython.readthedocs.io/en/latest/index.html)
HMMER 3.1b2 / hmmer tools: http://hmmer.org/ hmmscan and hmmsearch should be in path when running scripts that use HMM analysis
Python zelle graphics library v5: pip3 install --user http://bit.ly/csc161graphics (https://www.pas.rochester.edu/~rsarkis/csc161/python/pip-graphics.html)
Cytoscape 3.7.2 for analysis of locus clustering: https://cytoscape.org/ install clustermaker2 plugin: -> Apps -> App Manager -> search for clustermaker2, then install
Reference HMM files: https://www.kerfeldlab.org/uploads/2/6/6/7/26671774/reference_data.zip