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. 2004 Jul;78(14):7291-8.
doi: 10.1128/JVI.78.14.7291-7298.2004.

National center for biotechnology information viral genomes project

Yiming Bao  1 , Scott Federhen, Detlef Leipe, Vyvy Pham, Sergei Resenchuk, Mikhail Rozanov, Roman Tatusov, Tatiana Tatusova
Affiliations

National center for biotechnology information viral genomes project

Yiming Bao et al. J Virol. 2004 Jul.
No abstract available

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Figures

FIG. 1.
FIG. 1.
The growth of NCBI's Viral Genomes Project. The bars represent the numbers of new and all viral genome reference sequences in each quarter.
FIG. 2.
FIG. 2.
NCBI Viral Genomes Project main page (URL, http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html). The general introduction section containing the Influenza A virus replication scheme is followed by information on the number of available reference sequences and complete viral genomes. The latter is also a hyperlink to the complete list of available viral genomes; this link is duplicated in the lower right side as “Complete alphabetical list.” The numbers in the colored squares are the links to the lists of viral genomes grouped by major taxonomy divisions, where each number is the number of reference sequences in a particular division. Below is the virus group or family search box that allows one to retrieve the listing of all genomes belonging to a particular virus division, family, or floating genus. The lists for all of the taxonomy groups are available via the link “Genomes grouped by taxonomy” in the lower left-hand corner. Links from the blue sidebar menu include a general overview of viruses, virus reference sequences, statistics, “FAQ,” “Advisors,” “Help,” nucleotide and protein sequence retrieval tools, and alphabetical and taxonomic lists of available viral genomes. There are also links to external sites dedicated to virus biology, taxonomy, and nomenclature, as well as to other sequence databases.
FIG. 3.
FIG. 3.
The Viral Genomes web pages for the family Geminiviridae. Arrows indicate the direction of links between the web pages. (A) List of complete viral genomes for the family (taxonomy listing) (http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/10811.html). Viruses are listed in alphabetical order under each genus. (B) The genome summary page for Bean golden yellow mosaic virus (BGYMV) (http://www.ncbi.nlm.nih.gov/genomes/taxg.cgi?tax=220340). (C) Graphical view (circular) for the DNA A RefSeq sequence of BGYMV (http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=Genome&gi=10163 and http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=Genome&gi=10162). (D) VOG page for the family (http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/shagog.cgi?data=ssdna.defl&clust=SSDNA&fam=G). (E) Graphical representation of BLAST results for one of the protein clusters (http://www.ncbi.nlm.nih.gov/genomes/blu_all.cgi?data=ssdna.defl&cog=VOGs0100&phage=2&9626471).
FIG. 4.
FIG. 4.
A closer look at a viral genome: Enterobacteria phage P2. (A) Graphical view for the RefSeq of Enterobacteria phage P2 (http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=genome&gi=13510). The organism name on this page is linked to the corresponding page of the NCBI Taxonomy. The RefSeq accession number that starts with the letters “NC_” is linked to an Entrez record flat file view. There are also links to the following information: publications associated with the sequence (if any), the status (reviewed, validated, or provisional) of the genome record, and the hyperlinked accession number of the source sequence record. (B) A graphical view of proteins encoded in the phage genome (http://www.ncbi.nlm.nih.gov/genomes/altvik.cgi?gi=13510&from=0&to=33592&db=genome&x=15&y=17). (C) BLINK results for the Int protein (http://www.ncbi.nlm.nih.gov/sutils/blink.cgi?pid=9630357&cut=95). (D) List of Enterobacteria phage P2 proteins and their associated VOGs (http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/shagog.cgi?data=phogs.defl&clust=PHOG&org=Y).
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