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Protocols

IRD specifications

Information


Unique identifier OMICS_04512
Name IRD
Alternative name Influenza Research Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Influenza_Research_Database

Taxon


  • Viruses
    • Influenza A virus
    • Influenza A virus (A/Puerto Rico/8/1934(H1N1))
    • Influenza B virus

Documentation


Publications for Influenza Research Database

IRD citations

 (48)
library_books

How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin

2018
Nat Commun
PMCID: 5895760
PMID: 29643370
DOI: 10.1038/s41467-018-03665-3

[…] To infer the phylogenetic tree in Fig. , we downloaded one HA sequence per subtype from the Influenza Research Database, inferred the phylogenetic tree using RaxML with a GTR model, and visualized the tree using FigTree (http://tree.bio.ed.ac.uk/software/figtree/). The HA sequences used are […]

library_books

Identification and characterization of influenza A viruses in selected domestic animals in Kenya, 2010 2012

2018
PLoS One
PMCID: 5806879
PMID: 29425232
DOI: 10.1371/journal.pone.0192721

[…] tes was performed by the Virology, Surveillance and Diagnosis Branch, Influenza Division, CDC, Atlanta (). Homologs of HA genes of the Kenya swine isolates were obtained through BLAST searches in the Influenza Research Database for samples collected between 2009 and 2011. A list of isolates selected from the BLAST search and included in the phylogenetic analysis is provided ().HA nucleotide contig […]

call_split

Mouse Models of Influenza Infection with Circulating Strains to Test Seasonal Vaccine Efficacy

2018
Front Immunol
PMCID: 5797846
PMID: 29445377
DOI: 10.3389/fimmu.2018.00126
call_split See protocol

[…] he corresponding HI measurements were obtained either from the Francis Crick Institute Influenza Interim Reports or were kindly provided by John McCauley. HA sequences were downloaded from either the Influenza Research Database () or the EpiFlu database (). A phylogenetic tree of the HA sequences was estimated using BEAST () which incorporated the HKY substitution model, a coalescent model with co […]

library_books

Molecular subtyping of European swine influenza viruses and scaling to high throughput analysis

2018
Virol J
PMCID: 5761149
PMID: 29316958
DOI: 10.1186/s12985-018-0920-z

[…] enetic Analyzer (Life technologies, Carlsbad, CA, USA). Manual editing of sequences and assembly refinement were done with Vector NTI Advance 11.0 software (Life technologies, Carlsbad, CA, USA). The Influenza Research Database (IRD) was screened with BLASTN2 to identify sequences closely related to the HA and NA sequences. […]

call_split

Genetic evolution of influenza H9N2 viruses isolated from various hosts in China from 1994 to 2013

2017
PMCID: 5717095
PMID: 29184157
DOI: 10.1038/emi.2017.94
call_split See protocol

[…] All previously published sequences of H9N2 viruses isolated in China from 1994 to 2013 and related sequences were downloaded from the Influenza Research Database (www.FluDB.org), Global Initiative on Sharing Avian Influenza Data (www.gisaid.org) and the Influenza Virus Resource at the National Center for Biotechnology Information (w […]

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Influenza Herd Level Prevalence and Seasonality in Breed to Wean Pig Farms in the Midwestern USA

2017
PMCID: 5641542
PMID: 29075636
DOI: 10.3389/fvets.2017.00167
call_split See protocol

[…] es were annotated for completeness and functionality using the influenza virus sequence annotation tool (FLAN) (). H1 clade classification was done using the swine H1 clade classification tool in the Influenza Research Database (IRD) ().For H3 cluster classification, reference strains were obtained from the Influenza Virus Resource at the National Center for Biotechnology Information (NCBI) (). In […]


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IRD institution(s)
J. Craig Venter Institute, La Jolla, CA, USA; Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA; Department of Zoology, University of Cambridge, Cambridge, UK; Animal Health Service, Food and Agriculture Organization of the United Nations, Rome, Italy; Northrop Grumman Health Solutions, Chinakville, MD, USA; Vecna Technologies, Greenbelt, MD, USA; Bioinformatics Institute, University of Auckland, Auckland, New Zealand; Department of Pathology, University of California, San Diego, CA, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
IRD funding source(s)
This work was supported by National Institutes of Health/National Institute for Allergy and Infectious Diseases [HHSN272201400028C].

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