subsetting peptide sequence

[fazeliniah]

Dear MVP developer team,
Thank you very much for this great software. I am excited to test it for our HLA peptidome data. The published reports look fantastic. I don't think it is possible to download/export data from the HTML report (?) For example, I am interested to get the sequences of the "strong binders" peptides for one allele. What is the best way to do it?
Thanks

[kevinkovalchik]

Thank you for your interest in the software! You are correct that the HTML report itself doesn't contain the binding predictions. That is a good idea, though, so I might look into implementing it. However, when you run the tool, you get an option to save the predictions (using the "Link to analysis archive"):

The "analysis archive" contains netMHCpan predictions for each sample:

To find predictions for a specific allele, you can filter by the "Allele" column, or to find the predictions for a specific peptide you can filter by the "Peptide" column. The "Binder" column is defined by the EL_rank. If it is greater than 2.0 it is a non-binder, if it is less than or equal to 2.0 it is a weak-binder, and if it is less than or equal to 0.5 it is a strong binder.

I hope that is helpful! Let me know if you need anything else. As I mentioned, I will look into making these predictions available through the HTML report. That is a good idea.

Best wishes,
Kevin