Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Nov 15;34(22):3931-3933.
doi: 10.1093/bioinformatics/bty463.

ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins

Sandeep Kumar Dhanda  1 , Randi Vita  1 , Brendan Ha  1 , Alba Grifoni  1 , Bjoern Peters  1   2 , Alessandro Sette  1   2
Affiliations

ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins

Sandeep Kumar Dhanda et al. Bioinformatics. .

Abstract

Motivation: Datasets that are derived from different studies (e.g. MHC ligand elution, MHC binding, B/T cell epitope screening etc.) often vary in terms of experimental approaches, sizes of peptides tested, including partial and or nested overlapping peptides and in the number of donors tested.

Results: We present a customized application of the Immune Epitope Database's ImmunomeBrowser tool, which can be used to effectively aggregate and visualize heterogeneous immunological data. User provided peptide sets and associated response data is mapped to a user-provided protein reference sequence. The output consists of tables and figures representing the aggregated data represented by a Response Frequency score and associated estimated confidence interval. This allows the user to visualizing regions associated with dominant responses and their boundaries. The results are presented both as a user interactive javascript based web interface and a tabular format in a selected reference sequence.

Availability and implementation: The 'ImmunomeBrowser' has been a longstanding feature of the IEDB (http://www.iedb.org). The present application extends the use of this tool to work with user-provided datasets, rather than the output of IEDB queries. This new server version of the ImmunomeBrowser is freely accessible at http://tools.iedb.org/immunomebrowser/.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Screenshots for the example output of the customized application of ‘ImmunomeBrowser’. (A) Tabular format listing all the different epitopes mapped to the given reference protein sequence. (B) Area plot for upper and lower bound CI for RF. The line plot shows the number of positive and negative assays or number of responder and not-responder subjects along the positions in reference protein. Hovering the mouse over any position in the reference protein in any of these plots will display the lower and upper bounds of the RF and number of assays/subjects count found as positive and negative (as shown in red rectangle)
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Alvarez B. et al. (2018) Computational tools for the identification and interpretation of sequence motifs in immunopeptidomes. Proteomics. doi: 10.1002/pmic.201700252. - PMC - PubMed
    1. Asgari S. et al. (2015) Rational design of stable and functional hirudin III mutants with lower antigenicity. Biologicals, 43, 479–491. - PubMed
    1. Dhanda S.K. et al. (2018) Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity. Immunology, 153, 118–132. - PMC - PubMed
    1. Jawa V. et al. (2013) T-cell dependent immunogenicity of protein therapeutics: preclinical assessment and mitigation. Clin. Immunol., 149, 534–555. - PubMed
    1. Kim Y. et al. (2012) A meta-analysis of the existing knowledge of immunoreactivity against hepatitis C virus (HCV). PLoS One, 7, e38028. - PMC - PubMed

Publication types

-