|
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
|
