NCI PSD Tools

Proviral Sequence Annotation & Intactness Test (ProSeq-IT)

• ProSeq-IT is a standalone tool designed for users to obtain provirus sequence annotation and computationally inferred sequence intactness without going through PSD.
• To use ProSeq-IT, users need to
  • Select a subtype (only B, and C currently)
  • Upload sequences in fasta format
  • Click submit
• If your file contains HXB2 (for subtype B reference) or MJ4 (for subtype C reference), please rename HXB2 or MJ4 to a different name before submitting your file.
• Sequences to be submitted cannot have ambiguous nucleotides like Y, R, N, etc.
• File name and sequence ID cannot have space in them.
Run ProSeq-IT

HIV Epitope Detector (HIVepitopeDetector)

• HIV Epitope Detector is a tool for detecting HIV epitopes based on Las Alamos National Laboratory Immunology Database (https://www.hiv.lanl.gov/content/immunology/tables/optimal_ctl_summary.html).
• To use HIVepitopeDetector, users need to
  • Select a gene from the pull down menu
  • Upload a fasta amino acid sequence file (no alignment is needed)
  • Click submit
• The results include
  • the frequencies of each epitope including mutations in a sample population.
  • a list of epitopes in each sequence in the following format: 812-821_SLLNATDIAV_SLLNtTaIvV_809-818 where the first set of numbers “812-821” is the HXB2 position of epitope SLLNATDIAV, and the last numbers “809-818” is the HXB2 position of the detected sample epitope “SLLNtTaIvV” in the submitted sequence. Lower cases are the mutations.
Run HIVepitopeDetector