Predict peptide binders from an ORF or protein sequence

[Stefan Barisic]

Hi all!

I read your paper in Nature Biotechnology recently and I am interested in trying out your algorithm.

Does HLAthena have a feature to use an entire ORF or a protein as an input, and to predict good HLA binding peptides from those larger sequences?

It seems it can only predict already given peptides (or I am missing something?). I know that I could "chop" my protein into overlapping peptides using some other tool and use that list of peptides to run a batch screen on HLAthena, but was wondering if HLAthena has it already automated?

Thanks!

Stefan

[Sisi Sarkizova]

Hi Stefan,

HLAthena does support this scenario - you can input sequences in a fasta format and they will be chopped up into peptides before predictions are done. From the predict tab you can download a sample fasta file to get started. Please keep in mind that the sequences should only contain the 20 standard amino acid symbols (e.g. no 'X's). For more details please see http://www.hlathena.tools/ -> Predict -> How to. 

Let me know if you have further questions,

Sisi

  

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