2.2.5. Essential proteins and virulence factors

Input: localized.fasta Output: virulence.fasta - Proteins from ‘localized.fasta’ that have adequate matches in both VFDB (Virulence Factor Database) and DEG . Brief Summary: Filter resulting proteins based on their expected virulence.

The last step in the pipeline - which is intended to return a small number of candidates that we can review manually - is to select only the remaining proteins that are likely to be essential and virulence factors. This can be done through methods similar to the ones used in [Homologous Protein Removal] using the Database of Essential Genes and the Virulence Factor DataBase:

Note that DEG may have some entries where the sequence of the protein reads “Not available” instead of a valid amino acid sequence. To address that, the script below processes all entries and removes the ones that don’t contain a full sequence, ensuring DIAMOND can read the final file.

Parameters for the matches are once again taken from similar pipelines in literature. The ‘virulence.fasta’ file has 21 candidate proteins, which need to be manually analyzed.