pirl-unc / mhcgnomes / 33480009888
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coverage: 89.417%. Remained the same
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Establish 11 more prefixes from GenBank (#131) (#169)

The Iibi finding in #165 came from searching GenBank nuccore, where deposited
records name species prefixes at allele level. I then reported the remaining 30
entries as "could not establish" having searched only PubMed and the IPD group
tables. Running the same sweep across all of them establishes eleven.

A query shape hid two of those. The first pass asked for
"<species>"[Organism] AND (<prefix> OR MHC OR histocompatibility), so for
species with many MHC records the prefix hits fell outside retmax. Re-run with
the prefix required, Spau and Saal appeared. A zero from a query that could not
have found the answer is not a negative result.

Ten have allele-level names: Acda (Acda-DAB*1102), Crac (Crac-DB01..DB06),
Crpo (Crpo-DAB2), Ctau (Ctau-DRB23), Ctpe (Ctpe-DQA03), Ctta (Ctta-DRB26),
Ctto (Ctto-DQA02), Eqbu (DQB-Eqbu-DQB*0401), Orcu (Orcu-U2*05:02:01:01) and
Spau (Spau-DAA-214).

Saal is weaker and the entry says so: 98 records carry it as the isolate label
Saal_UBA_101..106, the species code and the salmonid class I locus
concatenated, rather than as an allele name.

Two negatives now have evidence instead of silence, pinned in the canary test.
Peafowl class II is deposited as "(B-LB) gene, B-LB-12 allele" -- the chicken
nomenclature, no Pacr anywhere. And Xetr does occur in GenBank, as clone tags
like Xetr-T2R54 for bitter taste receptors, not for MHC.

157 designated / 19 unknown, from 11/163 when the issue was filed.

0 of 36,752 corpus names change.

Claude-Session: https://claude.ai/code/session_012s4siLj2Vm33eNMGjNSazH

4250 of 4753 relevant lines covered (89.42%)

0.89 hits per line

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ID Job ID Ran Files Coverage
1 33480009888.1 41
89.42
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Source Files on build 33480009888