| # 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. |
|
|
|
|
