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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) multiple sequence alignment – H4 hemagglutinin nucleotide sequences from the aquatic duck and shorebird surveillance samples were aligned using the MUltiple Sequence Comparison by Log-Expectation algorithm and visualized using the IRD enhanced JalView. Bar graph of sequence conservation values along with the computed consensus sequence is shown at the bottom. Nucleotide residues shared by Alberta (ALB) duck and Delaware Bay (NJ, DE) shorebird isolates but not by the Minnesota (MN), North Dakota (ND), or Texas (TX) isolates are noted with red arrows. Residues unique to Alberta ducks (blue arrow) or shorebirds (green arrows) are also highlighted.
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fig04: Influenza Research Database (IRD) multiple sequence alignment – H4 hemagglutinin nucleotide sequences from the aquatic duck and shorebird surveillance samples were aligned using the MUltiple Sequence Comparison by Log-Expectation algorithm and visualized using the IRD enhanced JalView. Bar graph of sequence conservation values along with the computed consensus sequence is shown at the bottom. Nucleotide residues shared by Alberta (ALB) duck and Delaware Bay (NJ, DE) shorebird isolates but not by the Minnesota (MN), North Dakota (ND), or Texas (TX) isolates are noted with red arrows. Residues unique to Alberta ducks (blue arrow) or shorebirds (green arrows) are also highlighted.

Mentions: In addition to the integrated phylogenetic tree generation and visualization capability, the IRD also supports the generation and visualization of multiple sequence alignments. Multiple sequence alignments can highlight substitutions in common among the evolutionarily related sequences. The IRD uses the MUltiple Sequence Comparison by Log-Expectation (MUSCLE)43 algorithm to generate alignments, which can then be saved to the IRD Workbench and shared with collaborators. Alternatively, the user can visualize pre-computed and curated alignments that are stored on the IRD server to circumvent the alignment process, especially for large data sets. Visualization of sequence alignments in IRD is based on the Java alignment editor JalView44 (Figure 4).


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) multiple sequence alignment – H4 hemagglutinin nucleotide sequences from the aquatic duck and shorebird surveillance samples were aligned using the MUltiple Sequence Comparison by Log-Expectation algorithm and visualized using the IRD enhanced JalView. Bar graph of sequence conservation values along with the computed consensus sequence is shown at the bottom. Nucleotide residues shared by Alberta (ALB) duck and Delaware Bay (NJ, DE) shorebird isolates but not by the Minnesota (MN), North Dakota (ND), or Texas (TX) isolates are noted with red arrows. Residues unique to Alberta ducks (blue arrow) or shorebirds (green arrows) are also highlighted.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig04: Influenza Research Database (IRD) multiple sequence alignment – H4 hemagglutinin nucleotide sequences from the aquatic duck and shorebird surveillance samples were aligned using the MUltiple Sequence Comparison by Log-Expectation algorithm and visualized using the IRD enhanced JalView. Bar graph of sequence conservation values along with the computed consensus sequence is shown at the bottom. Nucleotide residues shared by Alberta (ALB) duck and Delaware Bay (NJ, DE) shorebird isolates but not by the Minnesota (MN), North Dakota (ND), or Texas (TX) isolates are noted with red arrows. Residues unique to Alberta ducks (blue arrow) or shorebirds (green arrows) are also highlighted.
Mentions: In addition to the integrated phylogenetic tree generation and visualization capability, the IRD also supports the generation and visualization of multiple sequence alignments. Multiple sequence alignments can highlight substitutions in common among the evolutionarily related sequences. The IRD uses the MUltiple Sequence Comparison by Log-Expectation (MUSCLE)43 algorithm to generate alignments, which can then be saved to the IRD Workbench and shared with collaborators. Alternatively, the user can visualize pre-computed and curated alignments that are stored on the IRD server to circumvent the alignment process, especially for large data sets. Visualization of sequence alignments in IRD is based on the Java alignment editor JalView44 (Figure 4).

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