MHC sequence data

[hammer]

The MHCflurry p/MHC binding predictor downloads MHC sequences from IPD and UniProt. I'm curious if they might be able to obtain this data from MRO instead, to maintain consistency with the rest of the IEDB data.

When I look into mro.owl, I see only 710 obo:MRO_sequence elements. That seems low. Am I looking in the right place for sequence data? Are there plans to import all sequences?

Thanks for your work on this resource!

[rvita]

Hi, We import our sequences from IPD and IMGT. We only have the MHC molecules that have been needed by the data present in the Immune Epitope Database (iedb.org) thus far. This is why the number seems low to you. But we do have plans to extend the MHC molecules in MRO to include all molecules with sequences in IPD and IMGT. For the sequences in UniProt, it can be difficult at times to be sure exactly which MHC molecule the sequence is for, so we were not planning on including those, unless we had additional information verifying which molecule it is.

[hammer]

Thanks for the quick reply! Do you know where we might find mouse MHC sequences if not in UniProt?

[rvita]

Good question. In the past we were unable to match the UniProt and GenBank entries to specific mouse MHC chains, but I have passed this question on to one of our bioinformatics guys to see if he has a better response. I'll get back to you soon.

[rvita]

Attached are the mouse MHC sequences that we have so far. We will make sure they get added to MRO too.
mouse_MHC_seqs.xlsx

[hammer]

Thanks @rvita! Can you comment on how these sequences were identified and evaluated for quality? I'm just trying to interpret this data in light of your previous comment about not including sequences from UniProt.