Index of HCV database tools organized by function

(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

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.

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

Background information

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 analysis

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.

Phylogenetics

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

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.

Immunology

PeptGen generate overlapping peptides from a protein sequence

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