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
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
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
SynchAligns
align overlapping alignments to one another
Primalign
align a nucleotide sequence (e.g., primer) to the complete genome alignment
Epilign
align a protein sequence (e.g., epitope) to the appropriate protein alignment
Pixel
This tool generates a PNG image of an alignment using 1 or more colored pixel(s) for each residue.
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
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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
Entropy
quantify positional variation in an alignment using Shannon Entropy
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
PeptGen
generate overlapping peptides from a protein sequence
Epitope Location Finder (ELF)
identify known and potential epitopes within immunologically reactive peptides
MotifScan
find HLA anchor motifs in protein sequences for specified HLA serotypes, genotypes or supertypes
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