Pipeline to fetch species assemblies from NCBI, run MacSyFinder per genome, and emit clean system/component matrices.
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Updated
Dec 4, 2025 - Python
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macsyfinder
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A computational pipeline for the pangenomic evaluation of Helicobacter pylori Type IV Secretion Systems (cag-PAI) and flagellar macro-architectures utilizing generalized hidden Markov models.
computational-biology proteomics hidden-markov-models structural-bioinformatics pangenomics pathogenicity-island helicobacter-pylori macsyfinder pan-secretome txsscan cag-pai t4ss type-iv-secretion-system bacterial-secretion-systems flagellar-assembly diderm-pathogens
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Apr 12, 2026 - Python
Pangenomic structural analysis of bacterial secretion machineries across Streptococcus pneumoniae isolates using optimized TXSScan hidden Markov models.
computational-biology bioinformatics-pipeline proteomics comparative-genomics hidden-markov-models pangenomics virulence-factors streptococcus-pneumoniae protein-translocation macsyfinder secretion-systems pan-secretome bacterial-pathogenesis txsscan
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Apr 12, 2026 - Python
A computational pipeline leveraging HMM-based probabilistic modeling to systematically identify, annotate, and map bacterial macromolecular secretion systems, conjugative transfer machineries, and CRISPR-Cas arrays across Bacteroidales proteomes.
computational-biology bioinformatics-pipeline comparative-genomics functional-genomics crispr-cas profile-hmm structural-annotation macsyfinder macromolecular-secretion-systems bacterial-secretion proteome-analysis
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Apr 7, 2026 - Python
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