## Description

This track shows known HIV-1 genes and regions based on data from HIV Sequence Database.

## Methods

Protein sequences from the Numbering Positions in HIV Relative to HXB2CG page at HIV Sequence Database were aligned against the HIV-1 reference genome (HXB2) using BLAT. Those alignments spanning less than 70% length of the protein sequence were discarded.

The variable regions (V2, V3, V4, and V5) of ENV are also marked according to the genomic position data found at http://www.hiv.lanl.gov/components/sequence/HIV/combined_search_s_tree/help.html#region.

The DNA sequences of the elements in the "Genes and Regions" track of the reference (HXB2) genome were aligned with the hivgne8v2(gp120) genome. The start and end positions of the resulting alignments were used to create this track.

## Credits

This track was produced at UCSC from protein sequence data obtained from the HIV Sequence Database.

## References

Korber BT, Foley BT, Kuiken CL, Pillai SK, Sodroski JG. Numbering Positions in HIV Relative to HXB2CG, p. III-102-III-111. In: Human retroviruses and AIDS 1998. Korber B, Kuiken C, Foley B, Hahn B, McCutchan F, Mellors J, Sodroski J, editors.

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.