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TRON-Bioinformatics / neofox

Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
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Interpreting results #18

Open ibrahimkurt opened 1 month ago

ibrahimkurt commented 1 month ago

Hi,

Can you please teach us a bit about how to navigate through the resulting output? I am aware that each column is reporting a different aspect of an immunological assessment, but is there an easy combined score that one can use by default to order and pick from the best neoantigen candidates?

It is my understanding that for SNVs, a good candidate is cloned into the mRNA vector as flanked by -/+ 13 amino acids. What would be the best cloning design for non-SNV neoantigen such as an indel/frameshift? Maybe clone the whole -13 amino acids till the first stop codon?

Thanks a lot.

franla23 commented 4 weeks ago

Hi @ibrahimkurt , There is currently no support for a score that combines all annotated features . Therefore, you might want to choose single or a combination of features from https://neofox.readthedocs.io/en/latest/03_02_output_data.html depending on your objective.

Regarding the second question, considering frameshift sequences until the first stop codon makes senses to cover all potential epitopes that could derive from such sequences.