The Virus Reference Genome project aims to provide molecular standards for viral genomic research. Viral RefSeqs start with one well-studied and/or best annotated full-length genomic sequence taken from GenBank. Each virus RefSeq genome is then curated by NCBI staff with the aid of outside advisors. The curation process results in the addition of relevant biological information, taken from the literature or other sequence records, as well as the correction of taxonomy and lineages. Viral RefSeqs are searchable in Entrez Genomes, which contains over 1,100 reference sequences for over 800 viral genomes. Access Viral Genomes using the link from the Related Resources section on the Entrez Genomes home page.

The Viral Genomes page includes a general introduction to viruses, a depiction of a scheme for the replication of influenza virus A and a variety of genome retrieval tools. Additionally, there are links to a complete alphabetical list of all reference genomes and to lists in which viruses are grouped by families/genera or genome type (e.g. dsDNA viruses, ssRNA posi-tive strand viruses). In the list, each virus name shown in green italics is hyperlinked to a graphical representation of the genome— the link to the actual genome record is accessible from the genome accession number (the number that begins with the letters “NC”). The rightmost column “Nbrs” of the viruses’ list leads to Genome Neighbors, which are related complete genomes found in GenBank. When available, links to the protein table for each virus genome are also displayed.

The Viral Genomes Finder, located on the main page and linked from the Tools section, allows the selection of all viruses, or viral genomes, that fall within a particular taxonomic node. The Query Tips offer help on how to formulate the search terms. For example, to retrieve all virus genomes within a particular taxonomic node, one must capitalize the first letter in the search word (i.e., “Flaviviridae”). To go to a Taxonomy Browser display of all viruses in a node, make sure the initial letter of the query is in lowercase.

Links from the blue sidebar menu include general over-views of viruses, statistics regarding virus reference genomes, FAQs, and help documentation on searching and viewing viral genome records. There are also links to external sites dedicated to virus biology, taxonomy and nomenclature, and sequences. The Help document presents samples of graphical formats and data layouts of the virus records in the database.

Click on figure to view enlarged version

Figure 1:Entrez Genomes graphical view of the viral RefSeq for the acute bee paralysis virus.

The sample record of Figure 1 shows the graphical view of a virus genome, which can have a linear or circular, monopartite or segmented architecture. The record gives a link to the GenBank flatfile record, the total number of nucleotides in the genome, and one or more literature citations. Also included are taxonomic information, additional comments about the reference sequence record, a reference to the source record from which it was derived, and the status of the record; either provisional or reviewed. Links in the blue sidebar lead to a table that lists the genes and protein products of the genome (Coding Regions), and to the Microbial Genomes BLAST program, which allows users to BLAST query sequences against the finished and unfinished microbial genomes database.

Virus genome reference sequences are added to the database daily and more analytical programs will be introduced in the near future. —VP

---