data(proteome): add 16 bacterial + viral reference proteomes

Foreign-antigen references for molecular-mimicry scans and peptide-flank
extraction, alongside the existing human/mouse proteomes.

- bacteria (5): E. gallinarum, R. gnavus, L. reuteri, E. coli K-12, S. aureus
- viruses (11): EBV B95-8, EBV AG876, CMV, VZV, HSV-1, HHV-6A, HHV-7,
adenovirus C, parvovirus B19, influenza A PR8, BK polyoma

All UniProt reference proteomes, gzipped, git-LFS tracked. proteome/README.md
records organism, proteome ID, taxid and sequence count for each.

Note: UP000007639 is Epstein-Barr virus strain AG876 (taxid 82830), NOT HHV-7.
It had been misfiled as HHV-7 upstream. The genuine HHV-7 reference proteome is
UP000098510 (strain RK, taxid 262398, 84 proteins), now included.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

DESCRIPTION.md

@@ -27,6 +27,7 @@ peptide–MHC already present in a primary dataset is dropped from CEDAR/Neopep.
 | `immunogenicity/hla_pop_freqs.tsv.gz` | — | HLA population freqs | EUR/ASN/AFR class-I (A/B/C) allele frequencies (AFND) |
 | `proteome/human.fasta.gz` | 4 | Human proteome (UP000005640) | self-reference proteome for similarity search |
 | `proteome/mouse.fasta.gz` | 5 | Mouse proteome (UP000000589) | C57BL/6 self-reference proteome |
+| `proteome/*_UP*.fasta.gz` | — | 16 bacterial + viral reference proteomes | foreign-antigen references for molecular-mimicry scans and peptide-flank extraction; see `proteome/README.md` |
 | `ligandome/viral_foreign_iedb.tsv.gz` | 2 | Viral ligandome (IEDB) | viral-source presented peptides (foreign reference) |
 | `ligandome/viral_orfs_gse272406.tsv.gz` | 1 | Pan-viral ORFs (GSE272406) | translated novel viral ORF proteins (foreign; *not* thymus self — spec mislabel) |
 | `ligandome/cancer_targets_tsarina.tsv.gz` | 3 | Cancer-testis antigens | curated shared tumor-antigen genes (tsarina) |

proteome/README.md

@@ -0,0 +1,36 @@
+# Reference proteomes
+
+UniProt proteomes used for source-protein lookup and peptide-flank extraction. All gzipped, git-LFS tracked.
+
+`human.fasta.gz` (UP000005640, 147,506 seqs) and `mouse.fasta.gz` (UP000000589, 54,857 seqs) are the full
+proteomes **including isoforms and TrEMBL** entries. The files below are canonical **reference** proteomes,
+fetched from UniProt (REST `?query=(proteome:<UPID>)&format=fasta`, or the reference_proteomes FTP).
+
+| file | organism | proteome | taxid | sequences | bytes (gz) |
+|---|---|---|---|---|---|
+| `ecoli_K12_UP000000625.fasta.gz` | *Escherichia coli (strain K12)* | UP000000625 | 83333 | 4,403 | 988,444 |
+| `egallinarum_UP000254807.fasta.gz` | *Enterococcus gallinarum* | UP000254807 | 1353 | 3,635 | 775,627 |
+| `mgnavus_UP000018690.fasta.gz` | *Mediterraneibacter gnavus (strain CC55_001C)* | UP000018690 | 1073375 | 2,942 | 666,125 |
+| `saureus_UP000008816.fasta.gz` | *Staphylococcus aureus (strain NCTC 8325 / PS 47)* | UP000008816 | 93061 | 2,889 | 577,723 |
+| `lreuteri_UP000001991.fasta.gz` | *Limosilactobacillus reuteri (strain DSM 20016)* | UP000001991 | 557436 | 1,865 | 401,750 |
+| `cmv_HHV5_UP000000938.fasta.gz` | *Human cytomegalovirus (strain Merlin)* | UP000000938 | 295027 | 168 | 42,838 |
+| `hhv6a_UP000009295.fasta.gz` | *Human herpesvirus 6A (strain Uganda-1102)* | UP000009295 | 10370 | 99 | 29,596 |
+| `ebv_UP000153037.fasta.gz` | *Epstein-Barr virus (strain B95-8)* | UP000153037 | 10377 | 92 | 27,660 |
+| `hhv7_UP000098510.fasta.gz` | *Human herpesvirus 7 (strain RK)* | UP000098510 | 262398 | 84 | 26,566 |
+| `ebv_AG876_UP000007639.fasta.gz` | *Epstein-Barr virus (strain AG876)* | UP000007639 | 82830 | 79 | 26,243 |
+| `hsv1_HHV1_UP000009294.fasta.gz` | *Human herpesvirus 1 (strain 17)* | UP000009294 | 10299 | 73 | 25,505 |
+| `vzv_HHV3_UP000002602.fasta.gz` | *Varicella-zoster virus (strain Dumas)* | UP000002602 | 10338 | 69 | 24,236 |
+| `adenovirusC_HAdV2_UP000008167.fasta.gz` | *Human adenovirus C serotype 2* | UP000008167 | 10515 | 45 | 9,028 |
+| `fluA_PR8_UP000009255.fasta.gz` | *Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)* | UP000009255 | 211044 | 13 | 3,378 |
+| `bkpyv_UP000008475.fasta.gz` | *BK polyomavirus* | UP000008475 | 1891762 | 6 | 1,238 |
+| `parvoB19_UP000006624.fasta.gz` | *Human parvovirus B19 (strain HV)* | UP000006624 | 648237 | 5 | 1,342 |
+
+Totals: 16,467 sequences across 16 proteomes (3,627,299 bytes gzipped).
+
+## Note on Epstein-Barr virus and HHV-7
+
+Two **EBV** strains are included: B95-8 (UP000153037, taxid 10377) and AG876 (UP000007639, taxid 82830).
+UP000007639 is EBV strain AG876 -- **not** HHV-7, despite what its proteome ID may suggest by adjacency.
+The genuine HHV-7 reference proteome is **UP000098510** (strain RK, taxid 262398, 84 proteins);
+UP000009246 (strain JI) exists but is flagged *Non Reference* by UniProt.
+

proteome/adenovirusC_HAdV2_UP000008167.fasta.gz

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proteome/bkpyv_UP000008475.fasta.gz

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proteome/cmv_HHV5_UP000000938.fasta.gz

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proteome/ebv_AG876_UP000007639.fasta.gz

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proteome/ebv_UP000153037.fasta.gz

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proteome/ecoli_K12_UP000000625.fasta.gz

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proteome/egallinarum_UP000254807.fasta.gz

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proteome/hhv6a_UP000009295.fasta.gz

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proteome/hhv7_UP000098510.fasta.gz

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proteome/parvoB19_UP000006624.fasta.gz

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proteome/saureus_UP000008816.fasta.gz

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