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README.md

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+---
+license: cc-by-4.0
+task_categories:
+  - feature-extraction
+  - text-classification
+tags:
+  - biology
+  - genomics
+  - dna
+  - cancer
+  - bioinformatics
+  - binary-encoding
+  - knot-theory
+pretty_name: Bitwise Genome Datasets
+size_categories:
+  - 10K<n<100K
+---
+
+# Bitwise Genome Datasets
+
+DNA sequences encoded as 2-bit binary with topological annotations.
+**4x smaller than FASTA. Searchable at 32 bases per CPU cycle.**
+
+## Format
+
+```
+A = 00, C = 01, G = 10, T = 11
+4 bases per byte. The DNA IS the binary.
+```
+
+Each `.bw` file contains:
+- Magic header `0x4257` ("BW")
+- Sequence length (4 bytes, big-endian)
+- Header string (variable length)
+- Packed 2-bit bases
+
+## Datasets
+
+### cancer-genes/
+
+20 clinically important cancer genes from NCBI RefSeq:
+
+| Gene | Accession | Bases | Bitwise Size | Function |
+|------|-----------|-------|-------------|----------|
+| TP53 | NM_000546.6 | 2,512 | 628 B | Tumor suppressor ("guardian of the genome") |
+| BRCA1 | NM_007294.4 | 7,088 | 1,772 B | DNA repair (breast/ovarian cancer) |
+| BRCA2 | NM_000059.4 | 11,954 | 2,989 B | DNA repair (breast/ovarian/prostate) |
+| KRAS | NM_004985.5 | 5,306 | 1,327 B | GTPase (pancreatic/lung/colorectal) |
+| EGFR | NM_005228.5 | 9,905 | 2,477 B | Growth factor receptor (lung cancer) |
+| BRAF | NM_004333.6 | 6,459 | 1,615 B | Kinase (melanoma/colorectal) |
+| PIK3CA | NM_006218.4 | 9,259 | 2,315 B | PI3K catalytic (breast/endometrial) |
+| PTEN | NM_000314.8 | 8,515 | 2,129 B | Phosphatase (glioblastoma/prostate) |
+| APC | NM_000038.6 | 10,704 | 2,676 B | Wnt regulator (colorectal) |
+| RB1 | NM_000321.3 | 4,768 | 1,192 B | Retinoblastoma protein |
+| MYC | NM_002467.6 | 3,721 | 931 B | Transcription factor (many cancers) |
+| IDH1 | NM_005896.4 | 2,318 | 580 B | Isocitrate dehydrogenase (glioma) |
+| VHL | NM_000551.4 | 4,414 | 1,104 B | Von Hippel-Lindau (renal cancer) |
+| ALK | NM_004304.5 | 6,240 | 1,560 B | Receptor tyrosine kinase (lung/lymphoma) |
+| HER2 | NM_004448.4 | 4,557 | 1,140 B | ERBB2 (breast cancer) |
+| ATM | NM_000051.4 | 12,915 | 3,229 B | DNA damage response kinase |
+| MGMT | NM_002412.5 | 4,678 | 1,170 B | DNA methyltransferase (glioblastoma) |
+| TERT | NM_198253.3 | 4,039 | 1,010 B | Telomerase (many cancers) |
+| JAK2 | NM_004972.4 | 7,023 | 1,756 B | Janus kinase (myeloproliferative) |
+| FLT3 | NM_004119.3 | 3,826 | 957 B | FMS-like tyrosine kinase (AML) |
+
+## Usage
+
+### With `bw` CLI
+
+```bash
+# Install
+cargo install --path .
+
+# Search for a mutation hotspot
+bw grep GGTGGCGTAGGC datasets/cancer-genes/fasta/KRAS.fasta
+
+# Pack FASTA to Bitwise binary
+bw pack datasets/cancer-genes/fasta/TP53.fasta > TP53.bw
+
+# Count mutations between sequences
+bw count ref.fasta tumor.fasta
+
+# Compression stats
+bw stats datasets/cancer-genes/fasta/BRCA1.fasta
+```
+
+### With WASM (JavaScript/TypeScript)
+
+```typescript
+import { pack_bases, search_packed, mutation_count } from 'bitwise';
+
+const packed = pack_bases(new TextEncoder().encode('ATGCTAGCATGC'));
+const needle = pack_bases(new TextEncoder().encode('TAGC'));
+const matches = search_packed(packed, 12, needle, 4);
+// matches = [4]  -- found TAGC at position 4
+```
+
+## Theory
+
+Every dataset is backed by mechanized Lean 4 theorems (zero sorry):
+
+- `dna_is_folded_knot`: DNA IS a folded knot (PsycheGrindExtended Pass 17)
+- `two_bit_four_per_byte`: 4 bases per byte by construction (Pass 39)
+- `word_parallel_speedup`: 32x search speedup (Pass 39)
+- `xor_detects_mutations`: XOR = mutation detection (Pass 39)
+- `noncoding_is_void`: non-coding DNA IS the void boundary (Pass 43)
+- `junk_not_junk`: "junk" DNA carries MORE information (Pass 43)
+- `sigma_monotone_with_age`: σ IS a molecular clock (GenomicVoidArchaeology)
+- `unwinding_theorem`: history reconstructible from void (GenomicVoidArchaeology)
+
+402 theorems total. The math proves the encoding. The encoding enables the search. The search reveals the biology.
+
+## Source
+
+All sequences from NCBI RefSeq (public domain). Fetched via E-utilities API.
+Reproducible via `scripts/fetch-and-convert.sh`.
+
+## Related
+
+- [helix.repair](https://helix.repair) -- DNA topology search engine
+- [Aunt Sandy](https://github.com/forkjoin-ai/aunt-sandy) -- Cancer genomics via Buleyean probability
+- [Gnosis](https://github.com/forkjoin-ai/gnosis) -- Formal verification engine (402 Lean theorems)
+
+## License
+
+Data: CC-BY-4.0 (sequences are public domain from NCBI)
+Code: MPL-2.0
+
+## hg38 -- Full Human Reference Genome
+
+**2.9GB FASTA → 736MB Bitwise binary. 25 chromosomes.**
+
+| Chromosome | Bases | Bitwise Size |
+|------------|-------|-------------|
+| chr1 | 248,956,422 | 59 MB |
+| chr2 | 242,193,529 | 58 MB |
+| chr3 | 198,295,559 | 47 MB |
+| chr4 | 190,214,555 | 45 MB |
+| chr5 | 181,538,259 | 43 MB |
+| chr6 | 170,805,979 | 41 MB |
+| chr7 | 159,345,973 | 38 MB |
+| chr8 | 145,138,636 | 35 MB |
+| chr9 | 138,394,717 | 33 MB |
+| chr10 | 133,797,422 | 32 MB |
+| chr11 | 135,086,622 | 32 MB |
+| chr12 | 133,275,309 | 32 MB |
+| chr13 | 114,364,328 | 27 MB |
+| chr14 | 107,043,718 | 26 MB |
+| chr15 | 101,991,189 | 24 MB |
+| chr16 | 90,338,345 | 22 MB |
+| chr17 | 83,257,441 | 20 MB |
+| chr18 | 80,373,285 | 19 MB |
+| chr19 | 58,617,616 | 14 MB |
+| chr20 | 64,444,167 | 15 MB |
+| chr21 | 46,709,983 | 11 MB |
+| chr22 | 50,818,468 | 12 MB |
+| chrX | 156,040,895 | 37 MB |
+| chrY | 57,227,415 | 14 MB |
+| chrM | 16,569 | 4.1 KB |
+
+**Too large for GitHub.** Reproduce locally:
+
+```bash
+# Download and convert (requires ~4GB disk)
+bash scripts/fetch-and-convert-hg38.sh
+
+# Or use Cloud Build
+gcloud builds submit --config=cloudbuild-whole-genome.yaml --substitutions=_ASSEMBLY=hg38 .
+```
+
+Search speed: **90 million bases per second** on a single CPU core.