PlasmidPlots

Borrelia burgdorferi, the bacteria responsible for Lyme disease, contains a large number of plasmids in its genome. These plasmids frequently contain copies of various gene families, some of which are essential for gene partitioning and replication. In A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi (full paper here), Casjens et al. plot these genes on the strain B31 as seen below (Figure 8 in the paper):

This program generates similar plots for any strain of any bacteria and any protein families, and can also show GC content or GC skew on the plots.

Installing

Prerequisites

Python

• Python 3
• imagemergetools
• matplotlib
• pyvirtualdisplay
• Biopython
• PIL

Other

• Firefox

Pip

pip3 install plasmidplots

Running

The program requires several text files to run, and a folder of example files can be found here. To run the program, open bash, navigate to the folder containing the files, and run the following command (this will take several minutes, depending on your computer):

python3 -m plasmidplots.pplots borrelia_urls.txt pfam.txt colors.txt subgroups.txt

To add GC content or GC skew to the plots, add --baseline gc or --baseline gcskew, respectively.