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Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.

BACKGROUND: The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. DESIGN: The Influenza Research Database (IRD, is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. RESULTS: To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. CONCLUSIONS: The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics.

Pubmed ID: 22260278 RIS Download

Mesh terms: Animals | Biomedical Research | Birds | Computational Biology | Databases, Nucleic Acid | Humans | Influenza in Birds | Influenza, Human | National Institute of Allergy and Infectious Diseases (U.S.) | Orthomyxoviridae | Orthomyxoviridae Infections | United States

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Immune Epitope Database and Analysis Resource

The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. Curation of peptidic and non-peptidic epitope data relating to all infectious diseases (including NIAID Category A, B, and C priority pathogens and NIAID Emerging and Re-emerging infectious diseases), allergens, autoimmune diseases, and transplant/alloantigens is current and constantly being updated. The database also contains Major Histocompatibility Complex (MHC) binding data from a variety of different antigenic sources and immune epitope data from the FIMM (Brusic), HLA Ligand (Hildebrand), TopBank (Sette), and MHC binding (Buus) databases. These databases and their investigators are hereby acknowledged as major contributors to the IEDB. Curation of epitopes related to allergies and other infectious diseases is in progress. Curation of autoimmune epitopes started in 2009. This site provides a collection of tools for the prediction and analysis of immune epitopes. It serves as a companion site to the Immune Epitope Database (IEDB), a manually curated database of experimentally characterized immune epitopes. The tools contained fall into the following categories: * T Cell Epitope Prediction Tools: This set of tools includes MHC class I & II binding predictions, as well as peptide processing predictions. * B Cell Epitope Prediction Tools: The tools here are intended to predict regions of proteins that are likely to be recogized as epitopes in the context of a B cell response. * Analysis Tools: The epitope analysis tools are intended for the detailed analysis of a known epitope sequence or group of sequences. Several IEDB Analysis tools can now be accessed via the RESTful (REpresentational State Transfer) Web Services. IEDB is located in the La Jolla Institute for Allergy and Immunology


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IVDB - Influenza Virus Database

IVDB hosts complete genome sequences of influenza A virus generated by BGI 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 aims to be a powerful information resource and an analysis workbench for scientists working on IV genetics, evolution, diagnostics, vaccine development, and drug design.


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