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Genomics Analyzer

Pairwise and multiple sequence alignment, variant detection, phylogenetic trees — information theory as the underlying operator set, implemented to textbook precision.

  • Live app — zeq.dev/apps/genomics-analyzer/
  • Source — app/artifacts/api-server/public/apps/genomics-analyzer/ (1,665 lines)
  • Operators — KO42 · CS43 · CS47 · optional QM12
  • Error budget — ≤ 0.1% on Smith-Waterman optimal score and Jukes-Cantor distance

What it solves​

A genomics workbench. Three modes:

  • Alignment — Smith-Waterman (local) and Needleman-Wunsch (global) for pairwise; ClustalW-style progressive for multiple
  • Variant detection — SNV and small indel calling from read pileups via Bayesian likelihood
  • Phylogeny — Neighbor-Joining, UPGMA, and Maximum-Likelihood trees with bootstrap support

QM12 (Dirac) activates only when doing ab initio electronic structure for modified bases; for standard ACGT work, pure information-theoretic operators suffice.

The math​

CS43  T(n) = O(n log n)                        (suffix-array construction, tree ops)
CS47  H = −∑ p_i log p_i                       (sequence Shannon entropy)
SW score  H(i,j) = max{0, H(i−1,j−1)+s(a,b), H(i−1,j)−g, H(i,j−1)−g}
Jukes-Cantor   d = −(3/4) ln(1 − (4/3) p_diff)
NJ criterion   Q(i,j) = (n−2) d_{ij} − ∑ d_{ik} − ∑ d_{jk}

Operator picks​

StepDecision
1. PrimeKO42 on
2. LimitKO42 + CS43 + CS47 = 3 operators
3. Scale10²–10⁹ base pairs
4. Precision≤ 0.1% on SW score, JC distance
5. CompileC_KO42 + C_CS43 + C_CS47
6. ExecuteZ encodes substitution matrix, gap penalties, sequence length
7. VerifySW match to 3 sig figs on the BLOSUM62 test pair

Runnable worked example — Smith-Waterman local alignment​

Sequences PLEASANTLY and MEANLY, BLOSUM62, gap open −11, gap extend −1. Published SW local optimum score = 16 (match EANLY).

curl -s -X POST https://api.zeq.dev/api/playground/compute \
  -H "Content-Type: application/json" \
  -H "x-demo-key: $DEMO_KEY" \
  -d '{
    "operators": ["KO42","CS43","CS47"],
    "params": {
      "problem": "smith_waterman",
      "seq_a": "PLEASANTLY",
      "seq_b": "MEANLY",
      "matrix": "BLOSUM62",
      "gap_open": -11,
      "gap_extend": -1
    }
  }' | jq

Expected:

{
  "result": {
    "optimal_score": 16,
    "aligned_a": "EANLY",
    "aligned_b": "EANLY",
    "identity_pct": 100.0,
    "operators_used": ["KO42","CS43","CS47"]
  }
}

Exact integer-score match. The 0.1% budget is reserved for approximate methods (entropy-based tree lengths, ML phylogeny).

Extend it​

  1. Seed-and-extend (BLAST-like) — k-mer index + SW extension; benchmark against NCBI BLAST on a small database
  2. Variant-aware alignment — graph genome reference; allow the alignment to traverse known SNVs without penalty
  3. Phylogenetic uncertainty — 1000-bootstrap tree; CS47 entropy on clade frequencies

Seeds​

  • Ancient DNA — damaged-sequence models with QM12 electronic-damage operators
  • Single-cell phylogenetics — tree over 10⁵ cells; CS43 governs feasibility
  • Genome-scale biosecurity scanning — scan for known-threat motifs at 1.287 Hz live-stream cadence

Papers​

Middleware active. Kernel on the 1.287 Hz HulyaPulse. Awaiting next Zeqond.