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HIV sequence database

Sequence Locator Explanation

Finding the location of a sequence

You may paste in any combination of nucleotide or amino acid sequences, or an uploaded file. The input box will also accept an accession number. The tool will locate and align your sequence(s) and display all results sequentially. You can mix nucleotide and amino acid sequences in your input.

The tool will, by default, also try to align the reverse complement of the submitted sequence(s). If a better match is found to the reverse complement than to the original sequence, the location and alignment of that match will be displayed. The results will prominently indicate that the reverse complement was used.


Retrieving a region by its coordinates

You may enter a single coordinate by entering that coordinate in the "from" box and checking the "include surrounding region" box. This will retrieve the 42 residues surrounding the given coordinate.

You may enter 'end' as a second coordinate with any valid first coordinate; the tool will retrieve the reference sequence for the specified region from the starting coordinate to the end of the sequence in that region.



You may specify nucleotide or protein output for both 'locate' and 'retrieve' requests; this is the only instance in which input from both parts of the form may be combined. Other combination requests will be rejected; you cannot, for instance, specify coordinates along with a pasted sequence, or ask for the surrounding region to be included in a request to locate the sequence for an accession number.

For a detailed description of the HIV and SIV numbering schemes, see:

For additional ways to obtain DNA and protein coordinates for genes, regions and features of HIV-1, HIV-2, and SIV, see:


last modified: Thu Dec 12 12:43 2013

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