title: Epitopemap: a web application for integrated whole proteome epitope prediction.
abstract: BACKGROUND
  Predictions of MHC binding affinity are commonly used in immunoinformatics for T cell epitope prediction. There are multiple available methods, some of which provide web access. However there is currently no convenient way to access the results from multiple methods at the same time or to execute predictions for an entire proteome at once.
  
  
  RESULTS
  We designed a web application that allows integration of multiple epitope prediction methods for any number of proteins in a genome. The tool is a front-end for various freely available methods. Features include visualisation of results from multiple predictors within proteins in one plot, genome-wide analysis and estimates of epitope conservation.
  
  
  CONCLUSIONS
  We present a self contained web application, Epitopemap, for calculating and viewing epitope predictions with multiple methods. The tool is easy to use and will assist in computational screening of viral or bacterial genomes.
authors.affiliation: School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland. farrell.damien@gmail.com.
authors.forename: Damien
authors.initials: D
authors.lastname: Farrell
authors.affiliation: School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland. stephen.gordon@ucd.ie.
authors.forename: Stephen V
authors.initials: SV
authors.lastname: Gordon
mesh_terms: D030562:Databases, Protein; D018604:Epitope Mapping / Q000379:methods*; D018984:Epitopes, T-Lymphocyte / Q000235:genetics* / Q000276:immunology / Q000378:metabolism*; D015395:Histocompatibility Antigens Class I / Q000235:genetics / Q000378:metabolism; D006801:Humans; D055261:Immunogenetic Phenomena; D011485:Protein Binding; D011506:Proteins / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D020543:Proteome / Q000235:genetics*; D012984:Software
chemical_list: D018984:Epitopes, T-Lymphocyte; D015395:Histocompatibility Antigens Class I; D011506:Proteins; D020543:Proteome