Skip to content

S. pneumoniae De Novo CPS Locus Discovery & Database Construction

This presentation validates LocusPredictor, Clusterer, Loci (GraphBatch), and LocusMatcher across a 4-stage Streptococcus pneumoniae capsular polysaccharide (CPS) locus discovery and de novo database construction pipeline.

Rather than relying on pre-trimmed reference databases or global nucleotide alignment, SeroGen extracts CPS biosynthetic operons de novo from unannotated sequences and whole chromosomes (including fragmented/contig-split assemblies), classifies divergent polysaccharide genes with GeneRoleClassifier, clusters them into functional orthogroups via hybrid Markov Clustering (Clusterer(mode="mcl")), and compresses the resulting Loci batch into an indexed de novo database and directed consensus pan-locus graph (Loci.as_pan_graph).

Key Takeaways

  • De Novo CPS Locus Discovery Across Mechanisms (LocusPredictor): Automatically segments both Wzy-dependent (CPS_WZY, anchored by wzg/cpsA–wze/cpsD, wzx, and wzy) and synthase-dependent (CPS_SYNTHASE, e.g., Type 3 capsule) loci directly from unannotated sequences and complete RefSeq chromosomes (100% recall on encapsulated strains and 100% specificity on the unencapsulated R6 rough negative control).
  • Hybrid CNN-Rescued MCL Orthogroup Clustering (Clusterer): Loci.cluster_genes combines RandstrobeIndex strobemer seeding, MMSEQS12 reduced-alphabet \(12^4\) CSR + ungapped BLOSUM62 diagonal prefiltering, SIMD-parallel Smith-Waterman-Gotoh (PairwiseAligner), role-gated GeneRoleClassifier active-site motif rescue, and sparse Markov Clustering (mode="mcl") to group divergent glycosyltransferases (GT), flippases (Wzx), and polymerases (Wzy) across the sequence twilight zone.
  • Zero-Copy Pan-Locus Graph Data Structures (Loci / GraphBatch): Bit-packed 32-bit GeneNodes (CLUSTER_ID, ROLE_ID, STRAND, IS_FRAMESHIFT) and IntergenicEdges (ORIENTATION, GAP_BIN) compress into a directed consensus pan-CPS CSR network via Loci.as_pan_graph() (visualized in 2D using LayoutEngine).
  • Fragmented Contig-Split Stitching & Novelty Detection: LocusPredictor(stitch_contig_splits=True) achieves 100% recovery across artificial intergenic and mid-ORF contig breaks (MatchType.FRAGMENTED_VARIANT), while LocusMatcher flags held-out novel locus architectures via Match.is_novel (MatchType.GENE_VARIANT) and falls back to the closest intra-serogroup relative.

Run Locally

# Present as interactive slideshow
uv run --with marimo --with altair marimo run scripts/benchmark_spneumo_db.py

# Edit notebook cells
uv run --with marimo --with altair marimo edit scripts/benchmark_spneumo_db.py

Comments