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About IVDB

Influenza virus (IV) is the causative agent of several serious influenza pandemics. 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. The Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS) has been sequencing various influenza viruses collected by scientists of different institutions from different parts of China. We have sequenced isolates of AIV subtype H5N1 from 1997 to 2005 in different hosts found in China, such as wild birds, poultry, water fowls, and mammals. BIG also has an on-going effort to generate more AIV/IV sequences. Meanwhile, significant international efforts in sequencing the viral isolates have been made worldwide that the number of IV sequences has been rising rapidly in public resources.

Frequent outbreaks of highly pathogenic avian influenza and the increasing data for comparative analysis require a central database specialized in influenza virus. We established the Influenza Virus Database (IVDB) to integrate information and to 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 and curates all other published influenza virus sequences after expert annotations. For the convenience of efficient data utilization, our Q-Filter system classifies and ranks all nucleotide sequences into 7 categories according to sequence content and integrity. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively. A searching system is developed for users to retrieve a combination of different data types by setting various search options. To facilitate analysis of the global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) is developed to display worldwide geographic distribution of the viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment tools and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to the pre-computed alignments and polymorphism analysis of influenza virus genes and proteins and presents the results by SNP distribution plots and minor allele distributions.

IVDB continues to make enhancements to its data quality, utility and functionality, aiming to be a powerful information resource and an analysis workbench for scientists working on IV genetics, evolution, diagnostics, vaccine development, and drug design.

Data Sources & Data Curation

As an integrated IV information resource, IVDB contains both BIG's data and data from public resources. BIG data have been submitted to NCBI and are being processed now. Data from NCBI Influenza Virus Resource (by U.S. National Institute of Health) form the backbone of the database. Since ISD (Influenza Sequence Database, by Los Alamos National Laboratory of the U.S.) accepts direct submission and contains some IV sequences that are absent in NCBI's Influenza Virus Resource, IVDB integrates additional 2,242 sequence segments from ISD. The current protein 3-D structural data are mainly from PDB (Protein Data Bank). More 3-D data will be acquired from our collaborators expertized in protein 3-D modeling.

All data in IVDB have been curated manually since data quality is of crucial importance for analysis. The main data curations include:

  • Examine annotations and source information from each sequence entry in public databases
  • Redefine host species (e.g. goose, coot instead of avian in general) and sampling locations (not only continents and country/regions, but also provinces/states of a nation), and store the information in searchable fields.
  • Match protein sequences with nucleotide sequences, and further annotate some predicted CDS and UTR.

    Furthermore, we utilized the self-developed Influenza Virus Sequence Quality Filter System (Q-Filter) to classify nucleotide sequences into 7 categories for the convenience of efficient data utilization.
  • Tools & Analysis

    As an IV analysis platform, except for the powerful searching system, IVDB provides a series of tools and viewers for analyzing genomes, genes and functions, polymorphisms, and phylogenetic relationship individually or in a comparative context.

    The tools include BLAST, multi-sequence alignment, phylogenetic tree builder, as well as self-developed IV Sequence Quality Filter System (Q-Filter) and IV Sequence Distribution Tool (IVDT). IVDB also offers instant access to the pre-computed multiple sequence alignments and sequence polymorphisms on both the nucleotide and protein level and presents the results by the SNP distribution plot and minor allele distributions.( For more information, see Help.)

    Authors of IVDB:

    CHANG Suhua         ZHANG Jiajie      LIAO Xiaoyun        

    Dr WANG Jing         Dr YU Jun         ZHU Xinxing         WANG Dahai         WANG Zizhu

    Thanks: RUAN Jue, YUAN Haifeng and LI Zhao for the technical support. We are indebted to all our collaborators, IV sample providers and other IV sequence producers for their contribution and kind support to the IVDB database.

    IVDB is supported by institutional grant from Beijing Institute of Genomics, CAS  Feedback