influenza virus ( iv ) is the causative agent of several serious influenza pandemics ( 1 ) .
recently , a highly pathogenic avian influenza virus ( aiv ; h5n1 ) has resulted in the death of more than 100 people and the slaughter of millions of poultry in asia , europe and africa ( world health organization , ) .
scrupulous surveillance and multidisciplinary interrogation of the viral migration patterns and evolution are crucial for preventing further casualties of humans and domestic poultry .
viral genome sequences provide essential information for understanding pathogenesis , diagnosis , and therapy of the virus .
since the iv genome mutates very fast from host to host and from year to year , tracing iv lineages and discovering the pattern of sequence variation provide a solid foundation for evolutionary and functional studies ( 2 ) .
genome - wide sequence analyses of iv have demonstrated various genotypes and proteotypes ( 3 ) and revealed multiple lineages and genetic re - assortment among viruses ( 4,5 ) .
the beijing institute of genomics ( big ) has been sequencing ivs collected by scientists from different institutions from different parts of china . since a highly pathogenic avian influenza a subtype h5n1 virus [ a / goose / guangdong/1/96/(h5n1 ) ]
was initially isolated from china and subsequently identified as a precursor of the hong kong 1997 aiv ( a / hong kong/156/97 ) ( 6 ) , china , especially the southern provinces , became one of the major foci for viral surveillance .
phylogenetic analysis of all gene segments of h5n1 viruses isolated in china and other countries allowed us to trace the ecological and genetic origins of aiv ( 7 ) and the mechanism of its transmission to southeast asia , europe and africa ( 8) .
we have sequenced isolates of aiv subtype h5n1 from 1997 to 2005 in different hosts found in china , such as wild birds , poultry , water fowl and mammals .
some of these strains have been published , such as those from tree sparrows in henan province in 2004 ( 9 ) and migratory birds in qinghai province in 2005 ( 10 ) .
significant international efforts in sequencing viral isolates have been made worldwide , so the number of iv sequences has been rising rapidly in public resources , such as the influenza virus resource ( ) at the national center for biotechnology information ( ncbi ) and the influenza sequence database ( isd ) at los alamos national laboratory ( 11 ) .
the ncbi influenza virus resource presents data obtained from the niaid ( national institute of allergy and infectious diseases ) influenza genome sequencing project as well as from genbank .
since most of the iv sequences are direct submissions , there is a growing need to curate and corroborate the data in order to analyze them effectively .
isd provides curated data , but it requires a subscription fee to obtain full access to the data and tools .
therefore , to provide a central iv - specialized database , which curates iv sequences , integrates information , and provides free online tools for data analysis , is of great importance .
the influenza virus database ( ivdb ) contains both big 's data and published iv sequences after expert curation to ensure a high standard of accuracy and completeness .
we have further developed tools and viewers to analyze and browse our data that include information concerning genomes , genes , polymorphisms , and phylogenetic relationships .
ivdb aims to be a powerful information resource and an analysis workbench for scientists working on iv genetics , evolution , diagnostics , vaccine development and drug design .
ivdb contains both big 's data ( big has an on - going effort to generate more aiv / iv sequences ) and data from public resources .
since isd accepts direct submissions and contains some iv sequences that are absent from ncbi 's influenza virus resource , ivdb incorporates an additional 1654 segment sequences from isd .
the data types hosted in ivdb include viral type / subtype , source information , nucleotide / protein sequence [ classified as complete genome , cds , untranslated region ( utr ) , three - dimensional ( 3-d ) structural data ] , sequence alignment , polymorphism , and categorized literature and web resources covering iv genomics , pathogenicity and epidemiology .
all data in ivdb have been curated manually since data quality is of crucial importance for analysis . to ensure adequate data quality , we first examine annotations and source information from each sequence entry in public databases . if we see inconsistencies or errors in the records , such as serotypes , we double check and proof - read the sequences .
sequences that do not have a genotype and subtype assigned are manually typed using phylogenetic analysis and blast tools .
second , we redefine host species ( e.g. goose , coot instead of avian in general ) and sampling locations ( not only continents and countries / regions , but also provinces / states ) , and store the information in searchable fields .
the detailed host information is crucial since phylogenetic studies of influenza a virus isolates have revealed that the viral genes form species - specific lineages ( 13 ) .
this is especially useful for aiv research since users have to distinguish wild birds from poultry , particularly the aquatic birds that are thought to be the primary carriers of influenza a viruses ( 13 ) .
third , we match protein sequences with nucleotide sequences , and further annotate some predicted cds and utrs .
users may browse the nucleotide and protein information simultaneously in one single record and trace back to the original records , if available , through hyperlinks .
furthermore , we developed the iv sequence quality filter system ( q - filter ) that classifies the nucleotide sequences into 7 categories of c1c4 and p1p3 , respectively , according to their sequence content ( cds , 5-utr , 3-utr ) and integrity ( c : complete or p : partial ) .
the c1c4 sequences have complete cds and differ in utrs ( such as without utr , with 5/3-utr or both ) .
all nucleotide sequences in ivdb have been classified and users may choose a specific category of data for analysis .
it is often useful to filter out short sequences since the length of nucleotide sequences ranges from dozens to thousands of base pairs .
this allows researchers to have a clear understanding of the sequence data and to choose high - quality data for their research .
the website also provides pre - computed alignments , phylogenetic trees , and variations in iv genes and proteins , which are grouped by host , subtype and segment .
results are presented through a graphical view of snp distribution or minor allele distribution , as well as tabular statistics on each nucleotide position compared with the consensus sequence .
users are not only able to search for sequence polymorphisms by host , subtype , and segment but also have instant access to pre - made alignments , phylogenetic trees , and geographical distributions on a world map .
the current version of ivdb contains 35 549 iv nucleotide sequences , most of which are from influenza a virus with 5670 h5n1 sequences .
. there are 2687 iv genome sets that contain all eight segments of type a and b iv , or all seven segments of type c iv .
more than 40 000 protein sequences , 118 protein 3-d structure records , and 200 groups of multiple sequence alignments with polymorphic sites highlighted are also included .
the statistics of nucleotide sequences available on september 16 , 2006 are shown in table 1 .
all data are freely available for downloading from our ftp site ( ) . statistics of nucleotide sequences in ivdb ( september 16 , 2006 ) the total number of nucleotide sequences from influenza a , b and c viruses .
ivdb provides a powerful search engine for users to retrieve different data types hosted in ivdb .
except for keyword search , users may combine various search options such as type ( influenza type a / b / c virus ) , serotype , host species , sampling place , sampling year , sequence length range , and sequence category classified by q - filter .
if users select the genomeset option , ivdb will display complete sets of sequence segments from selected iv strains .
a key enhancement is to allow users to browse results from the first search and to acquire more targeted data sets through a second search .
for example , users can acquire full - length ha sequences of h5n1 serotype isolated from chickens in guangdong province of china between 2003 and 2005 .
all search results can be saved to a personalized workset for users ' convenience in data management .
users can also maintain the workset themselves , delete , append or download data as well as apply successive analyses to the data using the tools provided .
as an iv data analysis platform , ivdb provides a toolkit and a series of viewers for analyzing iv genomes , genes , polymorphisms , and phylogenetic relationship individually or in a comparative context .
ivdb integrates blast tools for comparing user - supplied data ( e.g. workset ) with ivdb 's built - in databases , clustalw for multiple sequence alignment ( 14 ) , muscle ( 15 ) and phylip ( 16 ) for building phylogenetic trees . to facilitate analysis of global viral transmission and evolution
, we developed the iv sequence distribution tool ( ivdt ) for plotting worldwide geographic distributions of iv sequences .
it displays a zoomed - in geographic distribution of iv sequences from an upper level world map to a bottom - level of nation map . when the cursor is placed on a specific area of interest
, it will show sequence statistics in the area with information on hosts and years of sampling .
when the user clicks on the bottom - level map , it will display a list of hyperlinked sequence records that link to more details .
users may alternate easily from their search results to sequence distribution maps , and vice versa .
the ivdt 's sequence distribution map is a useful visual aid to display in which countries and at what density the samples have been collected in different regions of the world .
however , its results need to be interpreted with care since sampling biases are likely to be present .
all data and tools housed in ivdb are cross - linked , and the whole ivdb website forms an interrelated network as illustrated in figure 1 , which helps users to utilize , analyze , and understand the data more effectively and efficiently .
search results can be selectively saved in a personalized workset and subjected to successive data analyses , such as plotting geographical distribution , aligning multiple sequences , and building phylogenetic trees .
it consists of three hardware components , a world wide web server , a database server , and a server for sequence analysis .
the system is based on a mysql relational database , and the front end consists of a set of jsp scripts running on a tomcat web server . the q - filter and search engine
ivdt is similar to gis ( geographic information system ) with country coordinates stored in the database .
the blast and multiple sequence alignment tools run on clusters of super computers , and computational tasks are submitted by pbs ( portable batch system ) .
we are aiming to build a central iv - specialized database functioning not only as an integrated information resource , but also as an analysis platform for genetic , genomic , and phylogenetic research of ivs .
continuing efforts will be made to update iv sequences and incorporate new data and resources as soon as they become available .
ivdb will further classify iv sequences into host - specific clusters since ivs are isolated from a broad range of species . for analyzing transmission patterns in wild birds , ivdb will offer additional information on the geohydrologic environment , seasonal migrations , and migratory flyways of recorded wild bird populations throughout the world ( 20 ) , providing useful references for sequence variations from ivdb . in - depth
iv mutation analysis can be performed based on the pre - computed polymorphic results to identify synonymous / non - synonymous mutations and calculate silent ( ds ) and non - silent ( dn ) mutation rates . as an analysis platform for iv research
, ivdt continues to make enhancements to user interfaces , to improve infrastructures and functionality , and to add new applications . in order to identify the correlation between protein structure change and iv virulence ,
a key enhancement is to develop tools for displaying sequence variations in protein 3-d structures and to develop viewers for zooming in to a region of interest .
more analytical tools , such as epitope prediction software and a primer design pipeline , will also be integrated .
 frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses ( ivs ) . 
 we have established the influenza virus database ( ivdb ) to integrate information and create an analysis platform for genetic , genomic , and phylogenetic studies of the virus . 
 ivdb hosts complete genome sequences of influenza a virus generated by beijing institute of genomics ( big ) and curates all other published iv sequences after expert annotation . 
 our q - filter system classifies and ranks all nucleotide sequences into seven categories according to sequence content and integrity . 
 ivdb provides a series of tools and viewers for comparative analysis of the viral genomes , genes , genetic polymorphisms and phylogenetic relationships . 
 a search system has been developed for users to retrieve a combination of different data types by setting search options . to facilitate analysis of global viral transmission and evolution , the iv sequence distribution tool ( ivdt ) 
 has been developed to display the worldwide geographic distribution of chosen viral genotypes and to couple genomic data with epidemiological data . 
 the blast , multiple sequence alignment and phylogenetic analysis tools were integrated for online data analysis . 
 furthermore , ivdb offers instant access to pre - computed alignments and polymorphisms of iv genes and proteins , and presents the results as snp distribution plots and minor allele distributions . 
 ivdb is publicly available at 
INTRODUCTION
DATA CONTENT AND DATA CURATION
DATABASE ACCESS AND TOOLKIT
SYSTEM DESIGN AND IMPLEMENTATION
FUTURE DEVELOPMENT