The Influenza Research Database (IRD)
[Squires B., Macken C., Garcia-Sastre A. et al. BioHealthBase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence. Nucleic Acids Res. (2008) 36 (suppl 1): D497-D503]
doi:10.1093/nar/gkm905
/ref> 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 The Bioinformatics Resource Centers (BRCs) are a group of five Internet-based research centers established in 2004 and funded by NIAID (the National Institute of Allergy and Infectious Diseases.)[National Institute of Allergy and Infectious Diseases
The National Institute of Allergy and Infectious Diseases (NIAID, ) is one of the 27 institutes and centers that make up the National Institutes of Health (NIH), an agency of the United States Department of Health and Human Services (HHS). NIAID's ...]
(NIAID), a component of the National Institutes of Health
The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...
(NIH), which is an agency of the United States Department of Health and Human Services
The United States Department of Health and Human Services (HHS) is a cabinet-level executive branch department of the U.S. federal government created to protect the health of all Americans and providing essential human services. Its motto is ...
.
Data types in IRD
* Segment, protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
, and strain data
* Animal surveillance data
* Human clinical data
* Experimentally determined and predicted immune epitopes
An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The epitope is the specific piece of the antigen to which an antibody binds. The p ...
* Sequence Features[Noronha, J.M., Liu, M, Squires, R.B., et al. Influenza Sequence Feature Variant Type (Flu-SFVT) analysis: evidence for a role of NS1 in influenza host range restriction. J Virol. (2012) 86(10): 5857-5866]
doi:10.1128/JVI.06901-11
/ref>
* 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
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutio ...
: allows users to align segment/protein sequences using MUSCLE
* Sequence Alignment Visualization: uses JalView for sequence alignment visualization
* Phylogenetic tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
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:
References
External links
* {{official website, http://www.fludb.org/ IRD
Bioinformatics Resource Centers
The NIAID page describing the goals and activities of the BRCs
Influenza
Medical databases