Purpose: To find the position of your nucleotide or protein sequence(s) relative to the appropriate viral reference strain; or to give you a sequence based on a coordinate location.
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 Sequences of HXB2 (K03455) and Mac239 (M33262) HXB2 numbering | SIVmm239 numbering (review articles) HXB2 spreadsheet | SIVmm239 spreadsheet (spreadsheets with base-by-base annotation)