| --- |
| 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. |
|
|
