External links: Openhelix tutorial for Influenza on ViralZone
Surfing through ViralZone
Virus fact sheets
All viral fact sheets contain a "general" tab describing viral specific information:
-Molecular Biology (Virion and genome picture, gene expression, replication)
-Taxonomic and host informations
-Epidemiology informations (geography, associated diseases, vaccine etc..) UniProtKB/Swiss-Prot entries
The second and third tabs of the viral fact sheet contains a listing of all UniProtKB/Swiss-Prot protein entries for this viral family. The user can see entries either by protein name, or by strains. Species name is black when all the genome encoded proteins are displayed. When only part of the viral proteins are displayed, the species name is in grey.
DB links provides useful access to related web sites:
International Committee on Taxonomy of Viruses (ICTV) database
Nucleotide DB links to NCBI taxonomic pages, from which DDBJ/EMBL/GenBank nucleotides entries can be found.
Protein DB links to UniProtKB list of protein entries:
lists all reviewed entries (Swiss-Prot)
lists all unreviewed entries (TrEMBL)
handling and alignment tool
Alignment of any viral proteins can be produced easily in ViralZone. To illustrate this process, let's take the example of a user willing to compare an Ebolavirus GP protein sequence to the annotated references in UniProtKB. To reach the Ebolavirus fact sheet from the home page, type "Ebolavirus" in the "search virus" field. The search field proposes several species of Ebolavirus, either select one of those, or just hit return. The result gives links to the three levels of ViralZone virus sheets: Baltimore, family and genus. Click on Ebola-like viruses (genus). An alternative way could have been to click on the ssRNA(-) green button on the ViralZone home page and then click on the Ebolavirus link found under the Filoviridae family. To obtain an alignment of GP Ebolavirus proteins, scroll down on the genus sheet to "Matching UniProtKB/Swiss-Prot entries", and choose "reorder by protein" to get a list of proteins instead of list of strains. Find the third list "Envelope glycoprotein (GP1,2) (GP)". The four last sequences have a red dot meaning that 3D structures are available for these strains. Select all Ebolavirus GP proteins by hitting the "select all" button, and choose "align" on the menu beside. This action redirects to UniProt web site (www.uniprot.org) which displays a ClustalW alignment of the selected sequences. The alignment displays conserved amino-acids in grey, and can display more specific features. At the bottom of the page catch the "sequence annotation (Features) grey bar, and click on "show". Select "transmembrane" and a green colouring of this region appears on the alignment, "sites" will colour in yellow the cleavages and the antigenic sites, "mutagen" displays which amino acid has been experimentally mutated, etc... Details on these features can be accessed by clicking on a UniProtKB/SwisProt accession number (AC) at the left of the alignment, then reaching "features" of the corresponding entry. This tool makes it easy to map referenced features to a new laboratory sequence, by inserting any user sequence into this alignment. On the top left box "sequences", users can paste any sequence in FASTA format, and click align. The server will then align the new sequence to the UniProtKB entries. In no more than five clicks, users can access an annotated alignment for any viral protein set, and use it to map annotation on its own sequences.