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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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Add NetH2pan to the list of supported prediction algorithms #652

Open nruthen opened 3 years ago

nruthen commented 3 years ago

Would it be possible to add NetH2pan as a supported epitope prediction algorithm? NetH2pan is a standard benchmark/tool for MHC class I binding affinity predictions in mice.

ldanilova commented 1 year ago

netH2pan is included in netMHCpan 4.1. If I understand correctly, the current version of netMHCpan version included in pVACseq is 4.0. Is there a plan to update netMHCpan? We are also interested in running pVACseq on mouse data and the current version of valid alleles is missing one of the alleles that we need, H-2-Dq.

susannasiebert commented 1 year ago

@ldanilova it looks like the latest version of our Docker container already uses netMHCpan 4.1 and the IEDB API uses that version as well by default. I will update our documentation to reflect this. However, I don't see H-2-Dq as a supported allele for this method in IEDB. This would need to be addressed with IEDB directly. You might want to submit a ticket at https://help.iedb.org/hc/en-us.

yzhan360 commented 1 year ago

Hi, could I know how to check versions of netMHCpan and pVACseq that I am using with my current docker container?

susannasiebert commented 1 year ago

The pvactools version can be checked with pvactools -v. The netMHCpan version can be found in the IEDB source code README at /opt/iedb/mhc_i/README.