| # `proteome/` — sources |
|
|
| **Provenance lives in [`README.md`](README.md)** beside this file, and is not repeated here: it |
| carries every proteome's organism, UniProt proteome ID, taxid, sequence count and gzipped size, plus |
| the exact fetch form (UniProt REST `?query=(proteome:<UPID>)&format=fasta`, or the |
| reference_proteomes FTP). All 19 files are **experimental** sequence, unmodified. |
| |
| Summary: `human.fasta.gz` (UP000005640, 147,506 seqs) and `mouse.fasta.gz` (UP000000589, 54,857) are |
| the **full** proteomes including isoforms and TrEMBL; the other 16 are canonical **reference** |
| proteomes — 5 bacterial and 11 viral, 16,467 sequences in total — for molecular-mimicry scans and |
| peptide-flank extraction. |
| |
| ```zsh |
| mhcmatch bootstrap --proteome human,mouse,ecoli_K12_UP000000625 |
| ``` |
| |
| Two traps the README records and that are easy to reintroduce: |
| |
| - **UP000007639 is EBV strain AG876, not HHV-7**, despite the adjacency of the IDs. The genuine |
| HHV-7 reference is UP000098510 (strain RK, 84 proteins). |
| - Two EBV strains are present on purpose (B95-8 and AG876); they are not duplicates. |
| |
| **Size is the operational fact.** The human proteome has 68,389,335 nine-mer windows — every |
| position of every protein, because a source lookup is a question about *where* — and one seqtree |
| index over them costs ~12.6 GB. Ask for the lengths you need |
| (`mhcmatch.proteome.Proteome.find_sources` builds one index per distinct query length). |
|
|
