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HIV sequence database



HIV Sequence Locator

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.

Find the location of a sequence
Sequence organism Let program decide HIV SIV
Sequence base type Nucleotide Amino acid
Paste your input here
or upload your file
or enter accessions (For example; "AF073023, AY145955-AY145957")

-- OR --
Retrieve a region by its coordinates
Strain HXB2 SIVmm239
Enter coordinates: from to (Enter '1' and 'end' to retrieve the entire region.)
Region
Retrieve Nucleotide or Amino acid output
include surrounding region

Details: This tool has many uses:

  • find the start and end coordinates of your input sequence(s), relative to the reference strain HXB2 or SIVmm239,
  • show which genes or proteins your query touches,
  • show a graphical view of the location of your sequence(s) relative to the reference sequence,
  • display both the nucleotide sequence and protein translation of your input as it aligns to HXB2 or SIVmm239,
  • check the reverse complement of your input sequence, and report the orientation with the best match,
  • 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. 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)

last modified: Mon Dec 1 12:19 2014


Questions or comments? Contact us at seq-info@lanl.gov.

 
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