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.

    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.
    • Currently, this tool only detects the following epitopes: Download epitopes file
    • This tool is still under development, if you have any feedbacks, please contact Dr. Wei Shao at rid@mail.nih.gov.



© RID. Supported by Advanced Biomedical Computational Science (ABCS) at Leidos/FNLCR.