Search
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 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 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. 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 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. 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 Immunology
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 |