viruses are divided into two similar - sized groups depending on whether the virus particle contains dna or rna , and , as causes of human fatality , rna viruses are by far the more important ( 1 ) . new viral diseases continue to appear as a result of several changes in human activity : travel , population growth , interaction with wild habitats etc . well - known novel , or emergent , rna diseases include severe acute respiratory syndrome ( sars ) ( 2 ) , human immunodeficiency virus 1 ( hiv-1 ) ( 3 ) , and may come to include avian influenza h5n1 virus ( 4 ) . these emergent diseases are an important factor behind the increase in the number of genome sequences that ncbi treats as representing new species ( figure 1 ) . in 2005 , more than 200 new virus species were submitted to genbank ( more recent dates are less reliable because there is typically a delay between submission and public availability ) . as more emergent viruses appear , it is important to have a site that allows their genomes to be compared to those of known viruses . the origin of most major infectious diseases is unknown because of our ignorance of the diversity of pathogens in wild animals . this restricts our ability to both predict risks and develop treatments ( 5 ) . dates are the earliest given in the accession ( either of submission or publication ) . submissions after 2006 are excluded because accessions are made public typically only following publication and thus the frequency of submissions is more recent time periods is underestimated . dates are the earliest given in the accession ( either of submission or publication ) . submissions after 2006 are excluded because accessions are made public typically only following publication and thus the frequency of submissions is more recent time periods is underestimated . despite some advances ( 6,7 ) , the evolutionary history of rna viruses is in general poorly known , especially the deep phylogenetic relationships between virus families ( 8,9 ) . we believe that one of the reasons for this is a lack of easily available translated genes and genomes for all species , and the lack of aligned genome sequences representing different isolates of the same species . in addition to the need to facilitate greater comparative analysis of rna viruses is the need to link together the existing virus web sites and their underlying databases . there are many web sites that provide genomic data , tools for genetic analysis and/or biological information for some viruses ( see  links on our site home page ) . the rna virus database is intended to complement these other sites by providing basic genomic information and tools for all rna viruses and linking the user to more specialist sites , where they exist , e.g. for hiv-1 and hepatitis c virus ( hcv ) , we provide links to sites such as the los alamos laboratory on the main page for each of these viruses ( find by typing hiv-1 or hcv into the search window in the top toolbar ) . for such viruses , we do not duplicate the work of other groups by attempting to display the available diversity of genomes . we intend that the rna virus database should develop further as a hub for other sites and we therefore encourage other workers to contact us with details of their sites that they wish linked to ours . also , we encourage workers to  adopt a virus and improve and/or expand the information that we provide for individual species . this can be done by emailing us or getting involved directly in developing the database , which is an open source project available at our googlecode site ( http://code.google.com/p/rnavirusdb ) . some of the data and tools on the rna virus database can be found elsewhere , but not all of them can , e.g. ncbi 's genome site provides genomic overviews of virus species and pairwise alignments of other isolates to the reference sequence , but it does not provide multiple alignments or complete translated genomes as we do . similarly , its general entrez site provides pair - wise alignments of the query sequence and similar sequences in the database , plus a phylogenetic tree calculated from those distances ; however , no multiple alignment is built . we also corrected the ( few ) errors in the genbank entries , and our database records features such as rna editing ( 10 ) that make genome translation problematic . we have , therefore , created the rna virus database as a user - friendly site devoted to rna viruses , providing essential genomic data and tools ( discussed in more detail below ) and links to the other virus web sites . provide multiple whole - genome alignments , gene and whole - genome translations for all rna virus speciesidentification and taxonomic searching facilityguidance to other web resources . provide multiple whole - genome alignments , gene and whole - genome translations for all rna virus species identification and taxonomic searching facility guidance to other web resources . we provide multiple alignments of whole genomes ( as nucleotides ) for all species where genbank contains multiple representatives . our database , thus , currently has multiple alignments for approximately half the species ( available from the main page of any virus species under these alignments were made by downloading from genbank all complete ( or near - complete ) genomes using the bioperl genbank modules ( 11 ) . accidental mismatches were excluded by performing a preliminary alignment using blastalign ( 12 ) , which is designed to cope with non- or poorly homologous sequences and reports such matches . the sequences that showed clear homology to the ncbi reference sequences ( we used a cutoff of a maximum of 40% of positions being represented by gaps in the blastalign alignment ) , up to a maximum of 50 , were then aligned using clustalw ( default parameter values ) ( 13 ) . for species for which we have at least three sequences , a neighbor - joining tree was then constructed using paup ( with hky - adjusted genetic distances ) ( 14 ) , and this tree is displayed both as a pdf [ via the treegraph program ( 15 ) ] and using figtree , which is a new java - based tree - drawing application created by one of us ( rambaut , a . , unpublished data ) . our site allows virus nucleotide or amino acid sequences submitted by the user to be identified or , if the query is a new species , its closest relative to be found . in addition , the genomic location of any matched region of the library sequences is shown . for this we use ncbi 's suite of blast programs ( 16 ) ( go to the  blast link on the toolbar of the home page ) . once the most closely related reference species has been located , the query sequence can then be placed into a whole - genome multiple alignment for that species ( where such an alignment is present ) in order to show the query 's phylogenetic relationships to the genomes in our database ( go to ( i ) a blast of the query to the reference species sequence provides coordinates from the resulting pair - wise alignment . these coordinates are then used to select homologous regions from the reference multiple alignment , and a new multiple alignment is then built using clustalw along with a phylogenetic tree using paup as described above . ( ii ) blastalign ( described above ) is used to generate a new multiple alignment using the query sequence plus the sequences from the reference multiple alignment . figure 2.screenshots illustrating use of the rna virus database to investigate a submitted virus nucleotide sequence . screenshots illustrating use of the rna virus database to investigate a submitted virus nucleotide sequence . isolates , includes the biological data of the isolates used in the whole - genome multiple alignments [ except for hiv-1 , hcv and hepatitis b virus ( hbv ) , where we used manually built multiple alignments ; for these three species , accession numbers for the isolates are given in the supplementary data as accessionhivhcvhbv.xls ] . we provide amino acid sequences for all virus genes ( or , more strictly , for all open reading frames ) plus complete translated genomes for each virus species ( go to the translated genomes are intended to facilitate phylogenetic analysis of more distantly related viruses ( 9 ) . one feature that makes annotation of rna viruses difficult is that most species have some gene overlap ( 17 ) , i.e. where the same nucleotides code for two different genes by being read in two different frames . we , therefore , allow the user to select from three possible options for dealing with this feature : ( i ) have overlapped regions excised from the translated genome , ( ii ) have one only of any overlapped amino acid sequences represented or ( iii ) have all the amino acids sequences present , with overlapped sequences placed sequentially ( and thus the nucleotides represented twice ) . using a key word search of the genbank entries , and a standard reference work ( 18 ) where this did not reveal a match , the rna virus database is a php web application on top of a mysql database . php is available at http://www.php.net , but should come pre - installed on unix machines . all data have been taken from the ncbi 's genome and nucleotide sites at the following two urls . table names are in large bold font and interlinking column names are in small regular font . relationships of tables in the underlying mysql database . table names are in large bold font and interlinking column names are in small regular font . species names , nucleotide sequences and accession numbers were downloaded directly from genbank using bioperl modules , while further details of the virus  gene coordinates , taxonomic affinities etc.were subsequently extracted from the flatfile of all genbank entries that can be downloaded from the ncbi genome site ( 19 ) . our approach was to treat all entries in the ncbi virus genome sites as species and to follow their taxonomic classification , although we only give virus type ( e.g. single - stranded positive - sense , retrotranscribing ) , family and genus at our site . we , therefore , follow ncbi 's inclusion of hepadnaviruses , which include hbv , and caulimoviruses among the rna viruses despite their mature virion containing dna rather than rna ( their possession of reverse transcriptase clearly places them biologically and evolutionarily among the reverse - transcribing group of rna viruses ) . the php scripts can be accessed using subversion ( http://subversion.tigris.org/ ) from our googlecode site at http://code.google.com/p/rnavirusdb . the mysql database ( a gzipped 16 mb dump ) may also be downloaded from the same site for installation on the user 's computer if required . if required , the database can subsequently be updated by other users following instructions and perl scripts given in the supplementary material ( perl_scripts.tar ) . this updating involves a series of short intervening manual steps ( we find that complete automation of such processes is inefficient ) . we intend to update the database on at least a 6-monthly basis in order to include newly discovered viruses , and are currently working to incorporate biological and epidemiological data . as discussed in introduction , we are keen to collaborate with other groups over further developments of our database . wellcome trust ( to r.b . ) ; eu marie curie fellowship scheme ( to t.d.o . ) ; the royal society ( to a.r . )
the rna virus database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of rna virus . 
 it can identify submitted nucleotide sequences , can place them into multiple whole - genome alignments ( in species where more than one isolate has been fully sequenced ) and contains translated genome sequences for all species . 
 it has been created for two main purposes : to facilitate the comparative analysis of rna viruses and to become a hub for other , more specialised virus web sites . 
 it is available at the following four mirrored sites . 
 http://virus.zoo.ox.ac.uk/rnavirusdbhttp://hivweb.sanbi.ac.za/rnavirusdbhttp://bioinf.cs.auckland.ac.nz/rnavirusdbhttp://tree.bio.ed.ac.uk/rnavirusdb