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license: other
pretty_name: NCBI RefSeq Protein
size_categories:
- 100M<n<1B
task_categories:
- other
language:
- en
tags:
- biology
- proteins
- sequences
- fasta
- refseq
- ncbi
---
# NCBI RefSeq Protein
Normalized FASTA shards of the NCBI Reference Sequence (RefSeq) protein release.
Processed and uploaded by the [MegaData](https://github.com/) post-download pipeline
(internal repo). Original source: <https://www.ncbi.nlm.nih.gov/refseq/>.
## Statistics
| | |
|---|---|
| Source files | 1,725 |
| Shards | 1,725 |
| Compressed shard bytes | 72.74 GiB (78,108,688,857) |
| Records (per-source manifest sum) | 459,415,871 |
| Residues (per-source manifest sum) | 179,203,453,293 |
| Aggregate manifest `total_records` | 459415871 |
## Layout
```
.
├── _MANIFEST.json # aggregate manifest written by the pipeline
├── manifests/<source_slug>.json # per-source manifest (records, residues, shards)
├── metadata/<source_slug>.records.jsonl # per-record provenance
└── sequences/<source_slug>/shard-NNNNNN.fasta.zst
```
`<source_slug>` corresponds 1:1 with an upstream source archive; e.g.
`sequence_uniprotkb_uniprot_sprot.fasta.gz`.
## Loading
Stream every shard of one source (replace `<source_slug>` with the directory of
interest under `sequences/`):
```bash
hf download LiteFold/NCBI --repo-type dataset \
--include 'sequences/<source_slug>/shard-*.fasta.zst' \
--local-dir ./ncbi_refseq_protein
zstd -dc ./ncbi_refseq_protein/sequences/<source_slug>/shard-*.fasta.zst | head
```
Programmatic streaming with [`zstandard`](https://pypi.org/project/zstandard/):
```python
from huggingface_hub import snapshot_download
from pathlib import Path
import zstandard as zstd
local = snapshot_download(
repo_id="LiteFold/NCBI",
repo_type="dataset",
allow_patterns=["sequences/*/shard-*.fasta.zst"],
)
dctx = zstd.ZstdDecompressor()
for shard in sorted(Path(local).rglob("shard-*.fasta.zst")):
with shard.open("rb") as f, dctx.stream_reader(f) as reader:
buf = b""
while chunk := reader.read(1 << 20):
buf += chunk
*lines, buf = buf.split(b"\n")
for line in lines:
... # naive splitter; swap in your FASTA parser
```
## License
Public Domain (US Government work, NCBI RefSeq policy).
## Citation
> O'Leary NA, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44(D1):D733-45, 2016.
## Provenance
Built from the local manifest entry `ncbi_refseq_protein` of `manifests/atlas_download_plan.json`.
Pipeline source: `megadata-post normalize --dataset ncbi_refseq_protein`.
|