szpTyper is a Python tool designed for genotypic typing of Streptococcus equi genomes based on variants from the SzP (Streptococcus zooepidemicus M-like protein) gene. Leveraging NCBI's BLAST and Databases and BioPython libraries, szpTyper automates the process of querying and analyzing SzP gene sequences against a provided S. equi genome, aiding in the identification of specific SzP variants. Furhtermore, this tool alwoes for automated downlaod and updating of all certain SzP vartiants currently available on NCBIs database.
szpTyper currently inlcudes 201 distinct SzP genes.
- Python 3.x
- BioPython
- NCBI BLAST
You can install szpTyper using git:
git clone https://github.com/your_username/szpTyper.git
cd szpTyperszp_DB_download.py This will fetch all SzP Sequences that fulfill a sequence length of 900-1500 bp, download them in order to create a indexed database for querying.
szpTyper.py -i <input_genome_file.fasta> -o <output_directory> -f <szp_genes_fasta> -t <num_threads>szpTyper.py -i <file directory> -o <output_directory> --summary -f <szp_genes_fasta> -t <num_threads>With input variables being:
-i, --input: Path to the input genome file or directory.
-o, --output: Output directory for the results.
-f, --fasta: Path to the SzP genes FASTA file.
-t, --threads: Number of threads for BLASTN (default: 4).
-s, --summary: Creates a summary of all results if multiple genomes are scaned.
SzP Gene: The SzP gene, equivalent to the Streptococcus zooepimdicus M-Like protein gene, plays a crucial role in streptococcal infections and pathogenesis. szpTyper aids in understanding the genetic diversity of S. equi strains by identifying and characterizing SzP gene variants.
BLASTN Analysis: szpTyper utilizes NCBI's BLASTN tool to compare SzP gene sequences against the provided genome, determining the closest matches and their characteristics.
Molecular Epidemiology: With its ability to rapidly genotype S. equi strains, szpTyper facilitates molecular epidemiology studies, enabling researchers to track outbreaks, investigate transmission dynamics, and monitor genetic variations over time.
Veterinary Research: szpTyper is invaluable in veterinary research, aiding in the surveillance and control of S. equi infections in horses and other animals. Its high-throughput capability accelerates strain characterization and informs vaccination strategies.