A tutorial Jupyter Notebook illustrating how to use Biopython to identity and perform some basic characterization of a coronavirus genome sequence. Note, the use of a coronavirus genome is merely illustrative, the analyses are generic, and could be applied to any small genome.
Simply open the Notebook link here.
Or, view the notebook in nbviewer.
Via Binder :
First clone this repository:
git clone https://github.com/chris-rands/biopython-coronavirus;
cd biopython-coronavirus
Requires Python (version 3.6 or higher) with the jupyter
and biopython
modules. One of two options is recommended:
- Installation via pip
pip3 install jupyter biopython
For installation without root access add the --user
flag.
- Installation via conda
conda env create -f environment.yml
conda activate biopython-coronavirus
Open the Notebook as follows:
jupyter-notebook biopython-coronavirus-notebook.ipynb
- How is orf1ab cleaved into polypeptides? Can we predict this from the sequence?
- How do the researchers know (guess?) where orf1ab cleaves?
- nsp3 and nsp5 do it -- https://www.pnas.org/content/pnas/103/15/5717.full.pdf
- Which protein is the immune system responding to?
- "spike" and "nucleocapsid" -- http://www.cmi.ustc.edu.cn/1/3/193.pdf
- Are some people already immune from exposure to other coronavirus?
- Find the "furin cleavage site" in the "spike glycoprotein"
- It might be at the "PRRA" -- https://www.sciencedirect.com/science/article/pii/S0166354220300528
- Use ProP or PiTou to predict? -- https://en.wikipedia.org/wiki/Furin
- How similar are the other coronaviruses? (causes colds, not either SARS or MERS)
- alpha
- https://en.wikipedia.org/wiki/Human_coronavirus_229E (simpler, though targets APN)
- https://en.wikipedia.org/wiki/Human_coronavirus_NL63 (targets ACE2!)
- beta
- https://en.wikipedia.org/wiki/Human_coronavirus_OC43 (targets Neu5Ac)
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2095096/pdf/JIDMM17330.pdf
- Specifically, how similar is the N protein OC43, SARS v1, and SARS v2?
- https://en.wikipedia.org/wiki/Human_coronavirus_HKU1 (targets Neu5Ac)
- MERS-CoV
- SARS-CoV
- SARS-CoV-2
- https://en.wikipedia.org/wiki/Human_coronavirus_OC43 (targets Neu5Ac)
- alpha
- What adds the phosphate group to the N protein? Kinase?
_Figure 1. Phylogenetic tree showing the relationship of Wuhan-Hu-1 (circled in red) to selected coronaviruses. Nucleotide alignment was done with MUSCLE 3.8. The phylogenetic tree was estimated with MrBayes 3.2.6 with parameters for GTR+g+i. The scale bar indicates estimated substitutions per site, and all branch support values are 99.3% or higher.