Influenza Research Database

DisciplinesPublic database and tools

Websitewww.fludb.org

Influenza Research Database
Coverage
Influenza Research Database
Disciplines	Public database and tools
Links
Website	www.fludb.org

The Influenza Research Database (IRD)^[1]^[2]^[3] is an integrative and comprehensive publicly available database and analysis resource to search, analyze, visualize, save and share data for influenza virus research. IRD is one of the five Bioinformatics Resource Centers (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services.

Segment, protein, and strain data
Animal surveillance data
Human clinical data
Experimentally determined and predicted immune epitopes
Sequence Features^[4]
Predicted protein domains and motifs
Gene Ontology annotations
Computed sequence conservation score
Clade classification for highly-pathogenic avian influenza H5N1 HA sequences
3D protein structures
PCR primer data curated from literature
Experiment data from laboratory experiments and clinical trials
Phenotypic characteristic data curated from literature
Serology data
Host factor data

Analysis and visualization tools in IRD

BLAST: provides custom IRD databases to identify the most related sequence(s)
Short Peptide Search: allows users to find peptide sequences in target proteins
Identify Point Mutations: identifies influenza proteins having particular amino acids at user-specified positions
Multiple sequence alignment: allows users to align segment/protein sequences using MUSCLE
Sequence Alignment Visualization: uses JalView for sequence alignment visualization
Phylogenetic tree construction: calculates a tree using various algorithms and evolutionary models
Phylogenetic Tree Visualization: allows the color-coded display of strain metadata on a tree generated with one of several available algorithms and/or evolutionary models and viewed with Archaeopteryx
3D Protein Structure Visualization: integrates PDB protein structure files with sequence conservation score and IRD Sequence Features and provides an interactive 3D protein structure viewer using Jmol
Sequence Feature Variant Type (SFVT) analysis:^[4] provides a centralized repository of functional regions and automatically calculates all observed sequence variation within each defined region
Metadata-driven Comparative Analysis Tool for Sequences (Meta-CATS): an automated comparative statistical analysis to identify positions that significantly differ between user-defined sequence groups
Sequence Variation Analysis (SNP): pre-computed sequence variation analysis in all IRD sequences; also allows users to calculate the extent of sequence variation in user-specified sequences
PCR Primers/Probes: provides a repository of commonly used primers for influenza virus identification, and calculates the polymorphisms of all related IRD sequences at the primer positions
PCR Primer Design: allows PCR primer design for IRD and user-provided sequences
Sequence annotation: determines the user-provided nucleotide sequence's influenza type, segment number and subtype (for segments 4 and 6), and translates the nucleotide sequence
HPAI H5N1 Clade Classification: predicts the clade of highly pathogenic H5 HA sequences
ReadSeq: converts between various sequence formats
Data Submission Tool: allows users to submit influenza sequences, Sequence Features, and experimental data online
External Analysis Tools: displays a list and description of third-party tools for more specialized analyses
Personal Workbench to save and share data and analysis

Influenza Research Database

Analysis and visualization tools in IRD

References

External links

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