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What’s New in ViPR

September2011

Instant count of search results inViPRWe have just added the instant result countfeature, which enables you to search ViPR morequickly and more efficiently.

Now when you select search criteria on the ViPRsite, you will get instant count on how manyrecords match your search criteria without clickingthe“Search”button and running the search. Theinstant count is displayed just above the rightcorner of the light blue search box.

If there are too many or not enough search results,you can quickly change the search criteria on thesearch page.

Now you can browse genomestructures for pox and herpesviruses in ViPRViPR has launched GBrowse, a genome viewer thatprovides both bird’s eye and detailed views of

genomes and genome annotations. In thegenome browser window, you can search, scroll orzoom to a region of the genome, and view thegenome annotations including protein-codinggenes, Pfam domains, immune epitopes obtainedfrom the Immune Epitope Database (IEDB) and GCcontent. More annotations will be added in futurereleases.

There are two ways to access the GBrowse genomeviewer:

1. When a pox or herpes virus genome isviewable in GBrowse, there is a“View inGBrowse”link on the strain details page.Follow the link to display the genomebrowser.

2. On the Poxviridae or Herpesviridae page,mouse-over the“Analyze & Visualize”tab inthe navigation bar and click“View Genomesin GBrowse”. This will return a list of allgenomes that can be viewed in GBrowse.

Take a sneak peak of a herpes virus genome

displayed in GBrowse at:

http://www.viprbrc.org/brc/gbrowse.do?sequenceAccession=NC_009334&seqLength=172764&decorator=herpes&species=Human%20herpesvirus%204%20type%202

ViPR offers an easy way to searchfor virus Sequence FeaturesThe Sequence Feature Variant Type (SFVT)component is a unique tool in ViPR that can helpyou examine polymorphisms in virus proteins andidentify sequence variations that may correlatewith virus phenotypic characteristics. SFVTs arecurrently available for Dengue virus (serotype 2),Hepatitis C virus (subtype 1a), and Poxvirus(Vaccinia).

ViPR has launched an SFVT search page for you toquickly search for Sequence Features of interest.To access the search page, choose Dengue,Hepatitis C virus or Poxviridae from the ViPRhomepage, then mouse-over the“Search Data”tabin the navigation bar and click“Sequence FeatureVariant Types”.

The September 2011 release ofViPR is now available, visitwww.viprbrc.org/brc/

Virus Pathogen Resource (ViPR)

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