Immunogenetics

, Volume 57, Issue 11, pp 816–820 | Cite as

SNEP: SNP-derived Epitope Prediction program for minor H antigens

  • Mathias M. Schuler
  • Pierre Dönnes
  • Maria-Dorothea Nastke
  • Oliver Kohlbacher
  • Hans-Georg Rammensee
  • Stefan Stevanovic
Original Paper
First Online:
Received:
Accepted:

Abstract

The single nucleotide polymorphism (SNP)–derived Epitope Prediction program (SNEP) is now available to the public. It predicts minor histocompatibility antigens (miHAgs), which are T-cell epitopes containing polymorphic spots, from proteins listed in the SWISS-PROT database. SNEP recognizes polymorphisms (termed VARIANT or CONFLICT in SWISS-PROT) and predicts potential T-cell epitopes within a chosen distance around the polymorphic residue. The prediction algorithm is based on the SYFPEITHI T-cell epitope prediction program. SNEP is able to search for proteins according to their accession numbers, sequence stretches or gene names, for example. The predictions are available for several human leucocyte antigen class I and class II allelic products, which allow for a rapid and precise evaluation of potential miHAgs within polymorphic antigens.

Keywords

SNP Minor histocompatibility antigen T-cell epitope GvHD Epitope prediction 
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Notes

Acknowledgements

SNEP was established with the kind support of Merck KGaA., Darmstadt, Germany. We also acknowledge financial support from the European Union (Integrated Project ALLOSTEM, LSHB-CT-2004-503319) and the Deutsche Forschungsgemeinschaft (SFB 510 and 685). We would also like to thank Boris Töltl for his valuable comments.

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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Mathias M. Schuler
    • 1
  • Pierre Dönnes
    • 2
  • Maria-Dorothea Nastke
    • 1
  • Oliver Kohlbacher
    • 2
  • Hans-Georg Rammensee
    • 1
  • Stefan Stevanovic
    • 1
  1. 1.Abteilung Immunologie, Interfakultäres Institut für ZellbiologieUniversität TübingenTubingenGermany
  2. 2.Division for Simulation of Biological Systems, Wilhelm Schickard Institute for Computer Science/Center for BioinformaticsUniversität TübingenTübingenGermany

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