title: VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines.
abstract: BACKGROUND
  Vaccine development in the post-genomic era often begins with the in silico screening of genome information, with the most probable protective antigens being predicted rather than requiring causative microorganisms to be grown. Despite the obvious advantages of this approach--such as speed and cost efficiency--its success remains dependent on the accuracy of antigen prediction. Most approaches use sequence alignment to identify antigens. This is problematic for several reasons. Some proteins lack obvious sequence similarity, although they may share similar structures and biological properties. The antigenicity of a sequence may be encoded in a subtle and recondite manner not amendable to direct identification by sequence alignment. The discovery of truly novel antigens will be frustrated by their lack of similarity to antigens of known provenance. To overcome the limitations of alignment-dependent methods, we propose a new alignment-free approach for antigen prediction, which is based on auto cross covariance (ACC) transformation of protein sequences into uniform vectors of principal amino acid properties.
  
  
  RESULTS
  Bacterial, viral and tumour protein datasets were used to derive models for prediction of whole protein antigenicity. Every set consisted of 100 known antigens and 100 non-antigens. The derived models were tested by internal leave-one-out cross-validation and external validation using test sets. An additional five training sets for each class of antigens were used to test the stability of the discrimination between antigens and non-antigens. The models performed well in both validations showing prediction accuracy of 70% to 89%. The models were implemented in a server, which we call VaxiJen.
  
  
  CONCLUSIONS
  VaxiJen is the first server for alignment-independent prediction of protective antigens. It was developed to allow antigen classification solely based on the physicochemical properties of proteins without recourse to sequence alignment. The server can be used on its own or in combination with alignment-based prediction methods. It is freely-available online at the URL: http://www.jenner.ac.uk/VaxiJen.
authors.affiliation: Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St., 1000 Sofia, Bulgaria. idoytchinova@pharmfac.acad.bg <idoytchinova@pharmfac.acad.bg>
authors.forename: Irini A
authors.initials: IA
authors.lastname: Doytchinova
authors.forename: Darren R
authors.initials: DR
authors.lastname: Flower
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000942:Antigens, Bacterial / Q000737:chemistry* / Q000276:immunology; D000951:Antigens, Neoplasm / Q000737:chemistry* / Q000276:immunology; D001665:Binding Sites; D008969:Molecular Sequence Data; D011485:Protein Binding; D021122:Protein Subunits; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D022223:Vaccines, Subunit / Q000737:chemistry* / Q000276:immunology
chemical_list: D000942:Antigens, Bacterial; D000951:Antigens, Neoplasm; D021122:Protein Subunits; D022223:Vaccines, Subunit