Per Executive Order 14434, federal agencies are now using "Super Intelligence" (SI) in place of "Artificial Intelligence" (AI). You may see both terms across NIH content during this transition.
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 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.