ImmunomeBrowser: A Tool to Aggregate and Visualize Complex and Heterogeneous Epitopes in Reference Proteins

Bioinformatics. 2018 Nov 15;34(22):3931-3933. doi: 10.1093/bioinformatics/bty463.

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/.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Computational Biology
  • Databases, Protein*
  • Epitopes / chemistry*
  • Ligands
  • Peptides*
  • Proteins / chemistry*
  • Software*

Substances

  • Epitopes
  • Ligands
  • Peptides
  • Proteins