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PHAGE-I-Expanded: Proportion of Hla Associated Genomic Escape - Individual level (readme)

Given a set of HLA-associated polymorphisms, return the proportion of sites in an individual's sequence that are adapted to their HLA profile.


In the left-hand box, enter your HLA-associated polymorphism data in TAB-separated columns:
  1. HLA allele
  2. HIV codon position followed by amino acid
  3. Must be one of: "adapted" or "nonadapted"
  • In the right-hand box, the fist column must be a unique identifier for that patient/sequence
  • The next 6 columns (tab-delimited) should contain HLA type information such as "B*51:01" or "B5101". The order does not matter.
  • The last column should be the nucleotide sequence of that patient's HIV sequence. Translation is done in-house, and will attempt to resolve mixture nucleotides into all potential amino acids. If any of these potential amino acids matches any of the associated polymorphisms, it is considered a match.

Protein of Interest

Gag Pol Vif Vpr Vpu Tat Rev Env gp41 Nef