Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines

BMC Bioinformatics. 2007 Sep 26;8:361. doi: 10.1186/1471-2105-8-361.


Background: In an epitope-based vaccine setting, the use of conserved epitopes would be expected to provide broader protection across multiple strains, or even species, than epitopes derived from highly variable genome regions. Conversely, in a diagnostic and disease monitoring setting, epitopes that are specific to a given pathogen strain, for example, can be used to monitor responses to that particular infectious strain. In both cases, concrete information pertaining to the degree of conservancy of the epitope(s) considered is crucial.

Results: To assist in the selection of epitopes with the desired degree of conservation, we have developed a new tool to determine the variability of epitopes within a given set of protein sequences. The tool was implemented as a component of the Immune Epitope Database and Analysis Resources (IEDB), and is directly accessible at

Conclusion: An epitope conservancy analysis tool was developed to analyze the variability or conservation of epitopes. The tool is user friendly, and is expected to aid in the design of epitope-based vaccines and diagnostics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Computational Biology / methods*
  • Computer-Aided Design
  • Conserved Sequence
  • Diagnosis, Computer-Assisted
  • Drug Design
  • Epitope Mapping / methods*
  • Epitopes / classification*
  • Epitopes / ultrastructure
  • Humans
  • Internet
  • Sequence Alignment
  • Sequence Analysis, Protein
  • User-Computer Interface*
  • Vaccines / chemistry


  • Epitopes
  • Vaccines