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.
(For more information, mouse over the links)
Site search search our web site using the search box (top right of the page, below the virus)
Sequence search search for sequences by selecting from numerous criteria
Advanced search create your own search interface, access to all database info
Geography search retrieves HCV sequences based on geographical distribution
CTL epitopes search for CTL epitopes by protein, immunogen, HLA, author, keywords
T helper epitopes search for T helper epitopes by protein, immunogen, HLA, author, keywords
Antibodies search for HCV antibodies by protein, immunogen, AB type, isotype, author, keywords
Alignment and sequence manipulation
Translate nucleotide sequences to 1-letter amino acids
Gapstreeze Remove columns with more than a given % of gaps
Consensus compute a customizable consensus
Gene Cutter clip genes from a nucleotide alignment, codon-align and translate
HCValign aligns your sequence(s) using either the multiple alignment program MAFFT, or using the appropriate hidden Markov model.
SynchAligns align overlapping alignments to one another
Primalign align a nucleotide sequence (e.g., primer) to the complete genome alignment
QuickAlign (formerly Epilign and Primalign) aligns short nucleotide or protein sequences (e.g., primers, epitopes) to our prebuilt genome or protein alignments
Pixel This tool generates a PNG image of an alignment using 1 or more colored pixel(s) for each residue.
PepMap This tool can be used to map epitopes, functional domains, or any protein region of interest.
Genotypes Old and new HCV genotypes in the database
Geography geographic distribution of HCV database sequences
Alignments Curated sequence and reference alignments for all genes
Sequence locator find the standard numbering of your nucleotide or protein sequence in H77
HCV BLAST find sequences similar to yours in the HCV database
VESPA detect signatures: residues with different frequencies in two sequence sets
PCOORD multidimensional analysis of sequence variation
N-Glycosite find potential N-linked glycosylation sites in a protein alignment
SNAP calculate synonymous/non-synonymous substitution rates
Highlighter matches, mismatches, transition and transversion mutations, and silent and non-silent mutations in an aligned set of nucleotide sequences.
TreeMaker generate a quick-and-dirty phylogenetic tree
Search interface tree builder create a tree from sequences returned from database search
FindModel find which evolutionary model best fits your sequences
Branchlength calculates branch lengths between internal and end nodes based on a Newick treefile
Format Converter converts between 18 standard sequence formats
SeqPublish to make publication-ready alignments
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.
PeptGen generate overlapping peptides from a protein sequence