Entropy-Analysis

Conducting entropy analysis to measure the variability between the N and C terminal of sars-cov-2.

Reproduce

Procedure to reproduce results

1. download the nucleotide sequences from GISAID (EPI_SET_240302kp)
2. align sequences and isolate the N protein
3. translate the result to protein (we used MUSCLE alignment in Ugene)
4. convert the resulting fasta file to excel

• can use fasta_to_excel.py

5. run the entropy scripts

Data Cleaning Scripts

The other scripts here were used in the process of selecting the set of 1800 sequences:

• remove_low_coverage.py
  • remove sequences with more than 10 consecutive unknowns ("N") or deletions ("-")
  • only run on the N protein
• remove_duplicates.py
  • just remove any sequences which were duplicated by name in the fasta file
• equalize_variant_frequency.py
  • pick 150 for each named WHO variant