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Supplementary material for the NetCTLpan method (version 1.0):

Original method

NetCTLpan. Pan-specific MHC class I pathway epitope predictions.
Thomas Stranzl, Mette Voldby Larsen, Claus Lundegaard, and Morten Nielsen

The data sets used in the benchmark calculationis are given below in the FASTA format. For each entry is given the Uniprot of the protein "hosting" the epitope, the epitope sequence, and the HLA full-type information (if applicable), and the HLA supertype (if applicable).

An example showing part of such a fasta file is given below

>sp|O43707|ACTN4_HUMAN  AIDQLHLEY       HLA-A*0101      A1
MVDYHAANQSYQYGPSSAGNGAGGGGSMGDYMAQEDDWDRDLLLDPAWEKQQRKTFTAWC
NSHLRKAGTQIENIDEDFRDGLKLMLLLEVISGERLPKPERGKMRVHKINNVNKALDFIA
SKGVKLVSIGAEEIVDGNAKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPY
KNVNVQNFHISWKDGLAFNALIHRHRPELIEYDKLRKDDPVTNLNNAFEVAEKYLDIPKM
LDAEDIVNTARPDEKAIMTYVSSFYHAFSGAQKAETAANRICKVLAVNQENEHLMEDYEK
LASDLLEWIRRTIPWLEDRVPQKTIQEMQQKLEDFRDYRRVHKPPKVQEKCQLEINFNTL

SYFPEITHI 9mer training data set
SYFPEITHI 9mer evaluation data set
SYFPEITHI 8,10, and 11mer evaluation data set
SYFPEITHI HLA-C evaluation data set
HIV dataset
Supplementary Table. HLA supertype association for the HLA alleles used in the study

References

Stranzl T., Larsen M. V., Lundegaard C., and Nielsen M. NetCTLpan. Pan-specific MHC class I pathway epitope predictions. Paper Submitted