To navigate through the HPV genomes, we set up a "HPVomics genome browser" which facilitates graphical visualization of annotations.
Various tracks includes HPV reference genome, Genes, CDS, mRNA, exon, CpG islands, promoter, TATA box, CAAT signal, 5` UTR, repeat region, protein binding site, polyA signal sequence, and secondary structure information
The upper panel shows the positional scale (ruler) to navigate through genomes along with HPV reference sequence. Distinct annotation features were shown in separate color blocks.
This is an algorithm for the prediction of HPV B-cell and T-cell (MHC-I/II) epitopes
User can paste or upload peptide sequence to known the potentially of peptides to become epitopes
This is an interactive map of epitopes. In Epitope map, data is classified according the viral proteins with priority given to the HPV oncoproteins (E6, E7, E5).
It contains information such as IEDB id, start and end coordinates with gene region, epitope length, epitope sequence, and HLA allele type. Epitopes are mapped on the reference viral protein sequences.
HPVblast:: To find similarity and align query sequence to the HPV genomes and genes.
This tool allows user to select highly aligned regions of a DNA and protein multiple sequence alignment which can be used and more suitable for phylogenetic analysis.