proteome/ — sources
Provenance lives in 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.
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).