Influenza Research Database

Data types in IRD

• Segment, protein, and strain data
• Animal surveillance data
• Human clinical data
• Experimentally determined and predicted immune epitopes
• Sequence Features
• 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
• 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 analysis: 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 : an automated comparative statistical analysis to identify positions that significantly differ between user-defined sequence groups
• Sequence Variation Analysis : 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, 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