README.md

2020_Owen-BstA

About

Code corresponing to the paper:

Prophage-encoded phage defence proteins with cognate self-immunity (Owen, et. al., 2020)

doi: 10.1101/2020.07.13.199331

Data

• BstA homologs
  • Sequences
  • Homologs metadata
  • BstA profile-hmm
• Figures
  • Figure 2.A: All annotations
  • Figure 2.B: Annotation of genomic neighborhoods
  • Figure 2.C: BstA homologs alignment
• Raw data
  • The full raw data of the pipeline is generated as specified in ipynb_notebook/run_snakemake.ipynb.

Code

• Snakefile: A Snakemake pipeline which does the core genomic neighborhood analysis. It consists of downloading a specified sequence region from NCBI, annotating the region with Prokka, running hmmscan, and updating the annotations with BstA and Pfam hits. This produces the raw annotation data. A selection of these results was processed to create Figure 2.B.

2. ipynb_notebook/: Contains further details about how the pipeline is run, as well as additional processing of the raw data. The annotations analysis for Figure 2.A can be found in ipynb_notebook/load_all_tables.ipynb.