HIV Sequence Locator

Details: This tool has several purposes. It can find the start and end coordinates (relative to the reference strain HXB2 or SIVmm239) of your input sequence(s) and show which genes or proteins it covers, along with a graphical view of the location of your sequence(s) relative to the reference sequence. The tool will display both the nucleotide sequence and protein translation of your input as it aligns to HXB2 or SIVmm239. It will also check the reverse complement of your input sequence, and report the orientation with the best match. Another use is to retrieve a section of the HXB2 or SIVmm239 reference sequence based on its coordinates.

How to use: To find the coordinates for your sequence, either upload or paste your sequence (any format) in the box below. To retrieve the HXB2 or SIVmm239 sequence for a set of coordinates (see HIV coordinate map SIV coordinate map ) enter the coordinates and choose the region. To retrieve the entire gene or protein, enter coordinate values of "1" and "end". To retrieve a single nucleotide or range with its surrounding 42-nucleotide sequence, enter the single coordinate in the "from" field and check the box. For more details, see Sequence Locator Explanation.

Useful Links:
HXB2 numbering | SIVmm239 numbering (review articles)
HXB2 spreadsheet | SIVmm239 spreadsheet (spreadsheets with base-by-base annotation)