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

Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, Suarez D, Pickett BE, Zhang Y, Larsen CN, Ramsey A, Zhou L, Zaremba S, Kumar S, Deitrich J, Klem E, Scheuermann RH - Influenza Other Respir Viruses (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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Related in: MedlinePlus

Influenza Research Database (IRD) phylogenetic trees – (A) In the IRD enhanced version of the Archaeopteryx tree visualization tool, the user can color-code branch nodes based on a variety of different sequence annotation characteristics from the IRD database, in this case year of isolation grouped into 5-year intervals. Phylogenetic relationships between hemagglutinin nucleotide sequences from all H4 influenza subtype viruses isolated from aquatic ducks (Anatidae family) and shorebirds (Scolopacidae family) available in IRD surveillance records as of July 2011 are shown using the IRD “Quick Tree” maximum-likelihood estimation based on the HKY model of evolution. (B) An expanded view of the major 2005–2009 Minnesota (MN), North Dakota (ND), Texas (TX), Alaska (AK), and California (CA) duck branch. (C) An expanded view of the New Jersey (NJ) and Delaware (DE) shorebird branch with related Alberta (ALB) duck isolates from pre-2005.
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fig03: Influenza Research Database (IRD) phylogenetic trees – (A) In the IRD enhanced version of the Archaeopteryx tree visualization tool, the user can color-code branch nodes based on a variety of different sequence annotation characteristics from the IRD database, in this case year of isolation grouped into 5-year intervals. Phylogenetic relationships between hemagglutinin nucleotide sequences from all H4 influenza subtype viruses isolated from aquatic ducks (Anatidae family) and shorebirds (Scolopacidae family) available in IRD surveillance records as of July 2011 are shown using the IRD “Quick Tree” maximum-likelihood estimation based on the HKY model of evolution. (B) An expanded view of the major 2005–2009 Minnesota (MN), North Dakota (ND), Texas (TX), Alaska (AK), and California (CA) duck branch. (C) An expanded view of the New Jersey (NJ) and Delaware (DE) shorebird branch with related Alberta (ALB) duck isolates from pre-2005.

Mentions: The IRD supports numerous analysis tools, including the inference of maximum-likelihood phylogenetic trees using PhyML.41 A user can select a quick version of tree inference using default PhyML settings or specify the PhyML settings themselves. If the user does not know the best settings for PhyML for a particular set of sequences, the IRD custom software, ModelCompare, can be run to compare the fit of these data to a range of different models of evolution. The IRD also provides a customized tree viewer based on Archaeopteryx (http://www.phylosoft.org/archaeopteryx)42 that incorporates Archaeopteryx functions, such as re-rooting, subtree ordering, and branch swapping in addition to allowing the user to decorate the tree labels based on sequence metadata characteristics including subtype, host, country, or year of isolation derived from the IRD database (Figure 3).


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

Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, Suarez D, Pickett BE, Zhang Y, Larsen CN, Ramsey A, Zhou L, Zaremba S, Kumar S, Deitrich J, Klem E, Scheuermann RH - Influenza Other Respir Viruses (2012)

Influenza Research Database (IRD) phylogenetic trees – (A) In the IRD enhanced version of the Archaeopteryx tree visualization tool, the user can color-code branch nodes based on a variety of different sequence annotation characteristics from the IRD database, in this case year of isolation grouped into 5-year intervals. Phylogenetic relationships between hemagglutinin nucleotide sequences from all H4 influenza subtype viruses isolated from aquatic ducks (Anatidae family) and shorebirds (Scolopacidae family) available in IRD surveillance records as of July 2011 are shown using the IRD “Quick Tree” maximum-likelihood estimation based on the HKY model of evolution. (B) An expanded view of the major 2005–2009 Minnesota (MN), North Dakota (ND), Texas (TX), Alaska (AK), and California (CA) duck branch. (C) An expanded view of the New Jersey (NJ) and Delaware (DE) shorebird branch with related Alberta (ALB) duck isolates from pre-2005.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3345175&req=5

fig03: Influenza Research Database (IRD) phylogenetic trees – (A) In the IRD enhanced version of the Archaeopteryx tree visualization tool, the user can color-code branch nodes based on a variety of different sequence annotation characteristics from the IRD database, in this case year of isolation grouped into 5-year intervals. Phylogenetic relationships between hemagglutinin nucleotide sequences from all H4 influenza subtype viruses isolated from aquatic ducks (Anatidae family) and shorebirds (Scolopacidae family) available in IRD surveillance records as of July 2011 are shown using the IRD “Quick Tree” maximum-likelihood estimation based on the HKY model of evolution. (B) An expanded view of the major 2005–2009 Minnesota (MN), North Dakota (ND), Texas (TX), Alaska (AK), and California (CA) duck branch. (C) An expanded view of the New Jersey (NJ) and Delaware (DE) shorebird branch with related Alberta (ALB) duck isolates from pre-2005.
Mentions: The IRD supports numerous analysis tools, including the inference of maximum-likelihood phylogenetic trees using PhyML.41 A user can select a quick version of tree inference using default PhyML settings or specify the PhyML settings themselves. If the user does not know the best settings for PhyML for a particular set of sequences, the IRD custom software, ModelCompare, can be run to compare the fit of these data to a range of different models of evolution. The IRD also provides a customized tree viewer based on Archaeopteryx (http://www.phylosoft.org/archaeopteryx)42 that incorporates Archaeopteryx functions, such as re-rooting, subtree ordering, and branch swapping in addition to allowing the user to decorate the tree labels based on sequence metadata characteristics including subtype, host, country, or year of isolation derived from the IRD database (Figure 3).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Show MeSH
Related in: MedlinePlus