README.md

---
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

## Tools

### `bw` -- DNA ripgrep

Install the [Bitwise](https://github.com/forkjoin-ai/bitwise) CLI to search these datasets:

```bash
cargo install --path .  # from the bitwise repo

# Search for a pattern across a gene
bw grep GGTGGCGTAGGC cancer-genes/fasta/KRAS.fasta

# Count mutations between reference and tumor
bw count reference.fasta tumor.fasta

# Compression stats
bw stats cancer-genes/fasta/BRCA1.fasta
```

Search speed: **90 million bases per second** on a single CPU core.

### Aeon FlowFrame Protocol

These datasets stream natively as [Aeon FlowFrames](https://github.com/forkjoin-ai/aeon-flux):

```
stream_id = chromosome (1-25)
sequence  = genomic position
flags     = FORK | FOLD | VENT (structure type)
payload   = 2-bit packed bases
```

Wire = storage = memory. No serialization boundary.

### helix.repair

Search these datasets live at **[helix.repair](https://helix.repair)** -- a DNA topology search engine powered by Bitwise encoding and 402 Lean theorems.

## 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.