A simple BASH script for identification of Streptococcus uberis virulence factors from the draft genome
The database of virulence factors gene sequences is adopted from Vezina B, Al-Harbi H, Ramay HR, Soust M, Moore RJ, Olchowy TWJ, Alawneh JI. Sequence characterisation and novel insights into bovine mastitis-associated Streptococcus uberis in dairy herds. Sci Rep. 2021 Feb 4;11(1):3046. doi: 10.1038/s41598-021-82357-3. This publication should be cited when using Suberis_VF_blast.sh script.
The script is dependent only on local blast installation.
- install blast locally
for Ubuntu and Debian users
sudo apt install ncbi-blast+
others https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
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create /blastdb directory and put the file Suberis_vf_db_Vezina2021.fasta here
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build blast database in /blastdb
makeblastdb -in Suberis_vf_db_Vezina2021.fasta -parse_seqids -blastdb_version 5 -title "Suberis_vf_db" -dbtype nucl
- edit line 5 in Suberis_VF_blast.sh script to locate the blast database in your correct path (for example /home/$HOME/blastdb) and make the script executable
chmod +x Suberis_VF_blast.sh
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run Suberis_VF_blast.sh from directory containing your S. uberis draft genomes named *.fasta
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read output virulence_factors.tsv (tab separated columns). The columns are: sample virulence_factor length slen ppos query_coverage_%