Purpose: This tool finds the position of your nucleotide or protein sequence(s) relative to the appropriate viral reference strain. Or it can give you a sequence based on its coordinate location. See details below.
Details: This tool has many uses:
How to use: To find the coordinates for your sequence, either
upload or paste your sequence (any format) in the box.
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 and tips, see Sequence Locator Explanation.
Useful Links:Annotation resources for HIV-1, HIV-2, and SIV
HXB2 numbering |
SIVmm239 numbering (review articles)
HXB2 spreadsheet | SIVmm239 spreadsheet (spreadsheets with base-by-base annotation)