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.

Index of HCV database tools organized by function

(For more information, mouse over the links)


o Site search search our web site using the search box (top right of the page, below the virus)

o Sequence search search for sequences by selecting from numerous criteria

o Advanced search create your own search interface, access to all database info

o Geography search retrieves HCV sequences based on geographical distribution

Alignment and sequence manipulation

o Translate nucleotide sequences to 1-letter amino acids

o Gapstreeze Remove columns with more than a given % of gaps

o Consensus compute a customizable consensus

o Gene Cutter clip genes from a nucleotide alignment, codon-align and translate

o HCValign aligns your sequence(s) using either the multiple alignment program MAFFT, or using the appropriate hidden Markov model.

o SynchAligns align overlapping alignments to one another

o Primalign align a nucleotide sequence (e.g., primer) to the complete genome alignment

o QuickAlign (formerly Epilign and Primalign) aligns short nucleotide or protein sequences (e.g., primers, epitopes) to our prebuilt genome or protein alignments

o Pixel This tool generates a PNG image of an alignment using 1 or more colored pixel(s) for each residue.

o PepMap This tool can be used to map epitopes, functional domains, or any protein region of interest.

Background information

o Genotypes Old and new HCV genotypes in the database

o Geography geographic distribution of HCV database sequences

o Alignments Curated sequence and reference alignments for all genes

Sequence analysis

o Sequence locator find the standard numbering of your nucleotide or protein sequence in H77

o HCV BLAST find sequences similar to yours in the HCV database

o VESPA detect signatures: residues with different frequencies in two sequence sets

o PCOORD multidimensional analysis of sequence variation

o N-Glycosite find potential N-linked glycosylation sites in a protein alignment

o SNAP calculate synonymous/non-synonymous substitution rates

o Highlighter matches, mismatches, transition and transversion mutations, and silent and non-silent mutations in an aligned set of nucleotide sequences.


o TreeMaker generate a quick-and-dirty phylogenetic tree

o Search interface tree builder create a tree from sequences returned from database search

o FindModel find which evolutionary model best fits your sequences

o Branchlength calculates branch lengths between internal and end nodes based on a Newick treefile


o Format Converter converts between 18 standard sequence formats

o SeqPublish to make publication-ready alignments

o Protein Feature Accent provides an interactive 3-D graphic of selected HCV proteins; the user can map a sequence feature and see where it occurs spatially.


o PeptGen generate overlapping peptides from a protein sequence

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