Computational protocol: Genetic impact of vaccination on breakthrough HIV-1 sequences from the Step trial

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Protocol publication

[…] Known HIV-1 epitopes were included and potential CTL epitopes were predicted using NetMHC (http://www.cbs.dtu.dk/services/NetMHC/) and Epipred (http://atom.research.microsoft.com/bio/epipred.aspx/). NetMHC predicts binding of peptides to 4-digit HLA alleles; we accepted known epitopes reported at the Los Alamos National Laboratory HIV database (HIVDB) and variant epitopes that had identical HXB2 coordinates and were strong or weak binders. Epipred identifies known and potential HIV-1 CTL epitope motifs using 2-digit HLA information. HLA-specific epitopes were predicted in all HIV-1 proteins derived from the volunteers’ sequences and in the corresponding consensus founder sequences, based on each individual’s HLA genotype. Sequences from 3 volunteers were excluded (non-B subtype virus; non-male volunteer; no HLA-genotype). Epitopes were also identified in MRKAd5, HXB2 and CON_B04 sequences. […]

Pipeline specifications

Software tools NetMHC, EpiPred
Application Immune system analysis
Organisms Human immunodeficiency virus 1, Homo sapiens
Diseases HIV Infections
Chemicals Amino Acids, Vaccines