This repository contains the complete bioinformatic workflow and analytical framework utilized for the systematic profiling of bacterial secretion systems and related export structures across the Streptococcus pneumoniae pangenome. The dataset encompasses diverse clinical and environmental isolates, aiming to decipher the core and accessory components of the S. pneumoniae secretome.
Streptococcus pneumoniae represents a critically important human pathogen whose capacity for nasopharyngeal colonization and invasive disease relies extensively on surface-exposed and specifically secreted virulence factors. Given its monoderm architecture, the current computational approach is highly optimized to detect relevant translocation mechanisms including the Sec pathway, the Tat system, competence-associated pseudopili, and Esx secretion systems. Detection profiles for diderm-specific pathways (e.g., T3SS, T6SS) are leveraged effectively as robust negative controls within the search matrix.
The pipeline operates on complete, closed genomes derived from RefSeq. Algorithmic identification utilizes MacsyFinder, integrating calibrated TXSScan Hidden Markov Model (HMM) profiles to systematically search the proteomic dataset, thus producing rigorous genetic architectural quantifications of system presence and absence.
The analytical pipeline extracts independent hit frequency analyses, demonstrating the component-level conservation parameters for highly dynamic systems such as the Competence machinery (ComM).
Comprehensive visualization aggregates multiple features to establish a high-level systemic overview of pangenomic dynamics.
data/: Contains input sequences and intermediate logs.scripts/: Modular programmatic framework for parsing TXSScan records and rendering integrated computational visualizations.figures/: Core matrix of high-resolution graphic outputs encapsulating final system-level observations.
Conda execution environments and necessary run configurations are provided. To replicate the analysis, initialize the Conda environment specified inside the envs/ subdirectory, and execute the consecutive pipeline shell configurations hosted in scripts/.
This project is licensed under the MIT License - see the LICENSE file for details.