This directory contains information about influenza nucleoprotein CD8 T-cell epitopes drawn from an experimental database (the Immune Epitope Database) and from computational predictions (NetCTLpan).

Aichi68-NP.fasta -> the protein sequence of the A/Aichi6/1968 H3N2 influenza.

11639_NetCTLpan.txt -> Output from running NetCTLpan 1.1 server (http://www.cbs.dtu.dk/services/NetCTLpan-1.1/) on the Aichi68-NP.fasta protein sequence using the default settings (9-mer peptides) on the HLA supertypes. Generated on May-27-2012.

ImmuneEpitopeDatabaseQuery.csv -> Results of searching the Immune Epitope Database on May-28-2012. The query was for epitopes from the Source Organism Influenza A virus, the Immune Recognition of T Cell Response, the Host Organism of Homo sapiens, and the MHC Class I. The results are clustered at 90% identity.

mutations.txt -> Manually created file listing the mutations that occurred along the NP evolutionary trajectory from 1968 to 2007.

map_epitopes.py -> A Python script that analyzes the epitope data. It creates four *.txt files listing the epitopes and the epitopes by site. It also generates the plots in the directory "plots" which display information about these epitopes graphically.
