Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research

Abstract

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

Dynamic reassortments and genetic heterogeneity of the human-infecting influenza A (H7N9) virus

“…The percent identity of each virus genes was calculated by using the needle program in the EMBOSS package 24 . Data sets were obtained from the Influenza Virus Resource 25 and GISAID databases. For H5N1 data sets, we applied the database search with region/country and year as criteria.…”

Development of a seroprevalence map for Mycoplasma gallisepticum in broilers and its application to broilers from Comunidad Valenciana (Spain) over the course of two years (2009-2010)

“…In the literature, examples of the use of GIS technology in the prevention of avian diseases include Avian Influenza in several countries such as Italy and China (Ehlers et al 2003;Mannelli et al 2006;Chang et al 2007). However, until now, there has been no real-time informatics tool implemented to improve disease surveillance for M. gallisepticum in broilers in Comunidad Valenciana.…”

Computational analysis in Influenza virus

“…IRD is distinctive in the size and intensity of the data and analysis tools provided and in its approach to data and workflow integration that aid in the development of vaccines, therapeutics, and diagnostics [3] . A number of influenza-focused web-accessible databases exist: the NCBI Influenza Virus Resource (IVR) [8] , Global Initiative on Sharing Avian Influenza Data (GISAID) EpiFlu Database [9] , Korea Influenza Sequence & Epitope Database (KISED) [10] , the Influenza Virus Database (IVDB) [11] , and the OpenFlu Database [12] .…”