Virus Variation Resource--recent updates and future directions

Abstract

Virus Variation (http://www.ncbi.nlm.nih.gov/genomes/VirusVariation/) is a comprehensive, web-based resource designed to support the retrieval and display of large virus sequence datasets. The resource includes a value added database, a specialized search interface and a suite of sequence data displays. Virus-specific sequence annotation and database loading pipelines produce consistent protein and gene annotation and capture sequence descriptors from sequence records then map these metadata to a controlled vocabulary. The database supports a metadata driven, web-based search interface where sequences can be selected using a variety of biological and clinical criteria. Retrieved sequences can then be downloaded in a variety of formats or analyzed using a suite of tools and displays. Over the past 2 years, the pre-existing influenza and Dengue virus resources have been combined into a single construct and West Nile virus added to the resultant resource. A number of improvements were incorporated into the sequence annotation and database loading pipelines, and the virus-specific search interfaces were updated to support more advanced functions. Several new features have also been added to the sequence download options, and a new multiple sequence alignment viewer has been incorporated into the resource tool set. Together these enhancements should support enhanced usability and the inclusion of new viruses in the future.

Figure 1.

Influenza virus database search interface. The search interface is shown with the ‘Additional filters’ selection open. A number of search criteria have been selected, and two separate searches added to the ‘Query builder’. Selected search results are indicated by the check box to the left of the ‘Query builder’ display and can be downloaded directly in a variety of formats or loaded into the Virus Variation search results interface by depressing the ‘Show results’ button.

Figure 2.

Virus Variation search results interface. Results from a DENV database query are shown. The display includes a number of retrieved sequence descriptors including Accession, Length, Type, Disease, Genome region, Host, Country, Collection date and Virus name. Sequences can be selected and downloaded in a number of formats or used to construct an alignment or phylogenetic tree.

Figure 3.

Virus Variation multi-sequence alignment viewer. The results from a DENV database query were aligned and displayed in the Virus Variation multi-sequence alignment viewer. The top section of the alignment viewer includes a histogram that displays sequence and coverage variation across the alignment, a second histogram that plots the frequency of sequence differences with a shading scheme and highlights insertions and deletions with gaps and a feature table where protein names and other sequence feature identifiers are displayed. The alignment position is indicated above the histogram, and the region displayed in the lower section is highlighted by a gray box. The lower section displays the highlighted region in greater detail by default, but the magnification can be decreased or increased as desired by the user. Alignments are anchored to the consensus sequence by default, but any sequence can be selected as an anchor. Sequences identical to the consensus can be displayed as individual nucleotides or amino acids or replaced with dots—highlighting variations from the consensus.