HPVomics

• HPVomics Overview
• HPVomics provides a unique blend of potential therapeutic knowledge, HPV epitome, interactive genomic annotation browser and genomic analysis.


• HPVomics is classified in different sections represent individual components mainly therapeutics (i.e. siRNAs, sgRNAs, antiviral peptides etc.), vaccine epitopes (IEDB epitopes, MHC-I and -II binders, B-cell, CTL epitopes), genomes, genome browser, epitope map and tools.


• It also provide HPV epitome prediction algorithm "HPVepi" to predict the B-cell and T-cell (MHC-I and II) epitopes.


• Detail organization
  
• HPV Browser
• 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.


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• HPVepi
• 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


• Epitope Map
• 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.


• HPV BLAST
• HPVblast:: To find similarity and align query sequence to the HPV genomes and genes.





• ConBlock
• 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.