HCV Database
HCV sequence database

To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.

HCV 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 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
Enter coordinates: from to (Enter '1' and 'end' to retrieve the entire 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 H77,
  • 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 H77,
  • check the reverse complement of your input sequence, and report the orientation with the best match,
  • retrieve a section of the H77 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 H77 sequence for a set of coordinates (see HCV 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:
A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes. Kuiken C et al, Hepatology. 2006 Nov;44(5):1355-61.

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