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.

Note on the quality of the alignments The alignment of the major families (Dengue, West Nile, Yellow Fever, Japanese Encephalitis) is generally good, although the 3' NCR has some problems. Alignment of the polyprotein regions of more remotely related viruses is reliable for most viruses, but care should be taken with the Tamana bat virus and the other outliers. The alignment of the 3' and (to a slightly lesser extent) 5' NCRs is not trustworthy, and should probably not be used for analysis. Finally, the alignment of HCV-H with all others is very sketchy indeed; only occasional amino acid motifs show convincing similarity to the rest of the alignment. Please be sure to examine the alignment before using it in any regions you need. Work on this alignment is ongoing, and significant improvements will be announced in the News section of the website. To reformat the sequences, go to our Seq-Convert page.

Download nucleotide alignment as fasta. This is a codon-alignment, meaning all the gaps are edited to maintain the correct reading frame, so the alignment can be directly translated to amino acids.
Download amino acid alignment as fasta (polyprotein only)

The diversity graph below shows the % similarity of HCV-H to all other flaviviruses over the length of the (gapstripped) alignment; for visibility, only one representative of each major flavivirus clade was used. The graph was generated using Stuart Ray's program Simplot.

This is a neighbor-joining tree made from the alignment (ML distance model).

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