Influenza Research Database (IRD): A Web-based Resource for Influenza Virus Data and Analysis Victoria Hunt1*, R. Burke Squires1, Jyothi Noronha1, Brett Pickett1, Ed Klem3, Jon Dietrich3, Chris Larsen4 and Richard H. Scheuermann1,2 1Department of

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Influenza Research Database (IRD) A Web-based
Resource for Influenza Virus Data and Analysis
Victoria Hunt1, R. Burke Squires1, Jyothi
Noronha1, Brett Pickett1, Ed Klem3, Jon
Dietrich3, Chris Larsen4 and Richard H.
Scheuermann1,21Department of Pathology and
2Division of Biomedical Informatics, University
of Texas Southwestern Medical Center, Dallas,
Texas, United States 3Northrop Grumman
Information Technology, Rockville, Maryland,
United States 4Vecna Technologies Inc., College
Park, Maryland, United States
Abstract The Influenza Research Database (IRD)
Bioinformatics Resource Center (BRC)
(http//www.fludb.org) is a free, publicly
available resource that serves as a platform for
the discovery and development of influenza virus
vaccines, diagnostics and therapeutics. In order
to meet this goal, the IRD seeks to provide
researchers access to user-friendly interfaces
for data retrieval, data analysis, and
visualization tools. An overview will be
presented, briefly detailing the integration of
data types currently provided by this
bioinformatics resource including genomic data,
proteomic data, immune epitopes, surveillance
data, and other information that is useful in
understanding virulence and host-pathogen
interactions. Additionally, analysis tools and
other features accessible within IRD will be
described, allowing users to accomplish such
tasks as aligning multiple sequences, identifying
sequence similarities and variations, determining
phylogenetic relationships, visualizing proteins
structures, and also utilizing a private
workspace for saving and sharing analysis
results. Supported by NIH HHSN266200400041C

Workbench Researchers are able to store and
organize information from previous searches and
analyses into working sets by using their
personal Workbench. The workbench enables
working sets to be combined and/or shared with
user-designated collaborators.
IRD Homepage The IRD homepage directs users to
search pages, analysis and visualization tools,
and their personal workbench for user-friendly
navigation.
Search for Data in IRD Find and retrieve various
data types. Here a search is constructed for all
Influenza A sequences from segment 4 of the H1N1
subtypes in the USA (2009 only) from all hosts.
Results Summary results are returned in a
tabular format that displays a list of records
along with information about strain name,
subtype, host species, year, etc.

• Other IRD Tools and Features
• Sequence similarity search (BLAST)
• Geospatial representation of surveillance
  data
• Experiment data
• Experimentally-determined and IRD predicted
  epitope data
• Phenotype searches
• Browse the database for structural and
  functional sequence features in influenza
  proteins using the Sequence Feature Variant Type
  search
• Identify point mutations

Analysis After running a BLAST analysis using an
A/California/04/2009 (H1N1) query sequence, a
multiple sequence alignment (MUSCLE algorithm)
was conducted for comparison against 2008 H1N1
subtypes in the USA from different host species.
Alignments of the working set list were viewed in
both an html format and in JalView. This
assembled working set was also used to generate a
phylogenetic tree using the HYK model.
3D Structure Visualization Search and retrieve
3D protein structures for the influenza virus
that have experimentally-determined epitopes
obtained from the Immune Epitope Database (IEDB).
Above is a display of hemagglutinin complexed
with a neutralizing antibody. The
experimentally-determined B-cell epitope with
peptide sequence KRGPGSG is highlighted in
yellow. Also highlighted is the conservation
score where blue represents conserved regions and
red represents non-conserved regions.
Details Page Upon selection of the
A/California/04/2009, detailed information about
this strain is provided and has been integrated
onto one page for review.