“Influenza Research Database”的意思、由来-开放百科全书

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.

Data types in IRD

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

References

1. ^IRD Influenza Research Database BRC
2. ^Squires, R.B., Noronha, J., Hunt, V., et al. Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respi Viruses. (2012) 6(6): 404–416. doi:10.1111/j.1750-2659.2011.00331.x
3. ^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
4. ^¹Noronha, 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

External links

[https://web.archive.org/web/20111003095600/http://www.niaid.nih.gov/LabsAndResources/resources/dmid/brc/Pages/default.aspx Bioinformatics Resource Centers] The NIAID page describing the goals and activities of the BRCs

2 : Influenza|Medical databases